All studies
| ExclusiveBF | Non_exclusiveBF | No_BF | sum | |
|---|---|---|---|---|
| Bangladesh | 138 | 178 | 6 | 322 |
| Canada | 86 | 48 | 33 | 167 |
| Haiti | 37 | 11 | 0 | 48 |
| South Africa | 86 | 57 | 0 | 143 |
| USA(CA_FL) | 150 | 68 | 12 | 230 |
| USA(CA_MA_MO) | 38 | 66 | 116 | 220 |
| USA(NC) | 12 | 8 | 1 | 21 |
| All studies | 547 | 436 | 168 | 1151 |
All studies for stratified meta-analysis by birth mode
| Vaginal | C-section | sum | |
|---|---|---|---|
| Canada | 130 | 37 | 167 |
| Haiti | 42 | 6 | 48 |
| USA(CA_FL) | 162 | 65 | 227 |
| USA(CA_MA_MO) | 150 | 78 | 228 |
| All studies | 484 | 186 | 670 |
With Generalized additive mixed model (GAMM) fit and 95%CI.
Meta-analysis models based on adjusted estimate (adjusted for age of infant at sample collection) and standard error from linear mixed effect models.
RD 95%-CI %W(fixed)
Thompson et al 2015 ( USA(NC) ) 0.8754 [ 0.1366; 1.6142] 1.5
Wood et al 2017 ( South Africa ) 0.1214 [-0.2963; 0.5390] 4.7
Pannaraj et al 2017 ( USA(CA_FL) ) 0.2665 [ 0.0464; 0.4866] 17.1
Bender et al 2016 ( Haiti ) -0.1769 [-0.8203; 0.4664] 2.0
Subramanian et al 2014 ( Bangladesh ) 0.0568 [-0.0605; 0.1741] 60.2
Sordillo et al 2017 ( USA(CA_MA_MO) ) 0.7355 [ 0.3600; 1.1109] 5.9
Azad et al 2015 ( Canada ) 0.6149 [ 0.3048; 0.9250] 8.6
%W(random)
Thompson et al 2015 ( USA(NC) ) 7.3
Wood et al 2017 ( South Africa ) 13.4
Pannaraj et al 2017 ( USA(CA_FL) ) 18.7
Bender et al 2016 ( Haiti ) 8.7
Subramanian et al 2014 ( Bangladesh ) 21.0
Sordillo et al 2017 ( USA(CA_MA_MO) ) 14.5
Azad et al 2015 ( Canada ) 16.3
Number of studies combined: k = 7
RD 95%-CI z p-value
Fixed effect model 0.1913 [0.1003; 0.2823] 4.12 < 0.0001
Random effects model 0.3336 [0.0894; 0.5778] 2.68 0.0074
Quantifying heterogeneity:
tau^2 = 0.0702; H = 2.06 [1.42; 2.98]; I^2 = 76.4% [50.4%; 88.8%]
Test of heterogeneity:
Q d.f. p-value
25.40 6 0.0003
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Thompson et al 2015 ( USA(NC) ) | 0.0202100021212404 |
| Wood et al 2017 ( South Africa ) | 0.569010986228987 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.0176451947099079 |
| Bender et al 2016 ( Haiti ) | 0.589859305402284 |
| Subramanian et al 2014 ( Bangladesh ) | 0.342537683608756 |
| Sordillo et al 2017 ( USA(CA_MA_MO) ) | 0.000123424504683378 |
| Azad et al 2015 ( Canada ) | 0.000101690866421991 |
RD 95%-CI %W(fixed)
Thompson et al 2015 ( USA(NC) ) 0.8754 [ 0.1366; 1.6142] 1.5
Wood et al 2017 ( South Africa ) 0.1214 [-0.2963; 0.5390] 4.8
Pannaraj et al 2017 ( USA(CA_FL) ) 0.2665 [ 0.0464; 0.4866] 17.4
Subramanian et al 2014 ( Bangladesh ) 0.0568 [-0.0605; 0.1741] 61.4
Sordillo et al 2017 ( USA(CA_MA_MO) ) 0.7355 [ 0.3600; 1.1109] 6.0
Azad et al 2015 ( Canada ) 0.6149 [ 0.3048; 0.9250] 8.8
%W(random)
Thompson et al 2015 ( USA(NC) ) 8.1
Wood et al 2017 ( South Africa ) 14.8
Pannaraj et al 2017 ( USA(CA_FL) ) 20.4
Subramanian et al 2014 ( Bangladesh ) 22.9
Sordillo et al 2017 ( USA(CA_MA_MO) ) 15.9
Azad et al 2015 ( Canada ) 17.8
Number of studies combined: k = 6
RD 95%-CI z p-value
Fixed effect model 0.1988 [0.1069; 0.2908] 4.24 < 0.0001
Random effects model 0.3835 [0.1247; 0.6422] 2.90 0.0037
Quantifying heterogeneity:
tau^2 = 0.0726; H = 2.20 [1.49; 3.25]; I^2 = 79.3% [54.7%; 90.5%]
Test of heterogeneity:
Q d.f. p-value
24.11 5 0.0002
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Thompson et al 2015 ( USA(NC) ) | 0.0202100021212404 |
| Wood et al 2017 ( South Africa ) | 0.569010986228987 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.0176451947099079 |
| Subramanian et al 2014 ( Bangladesh ) | 0.342537683608756 |
| Sordillo et al 2017 ( USA(CA_MA_MO) ) | 0.000123424504683378 |
| Azad et al 2015 ( Canada ) | 0.000101690866421991 |
RD 95%-CI %W(fixed)
Wood et al 2017 ( South Africa ) 0.1214 [-0.2963; 0.5390] 4.8
Pannaraj et al 2017 ( USA(CA_FL) ) 0.2665 [ 0.0464; 0.4866] 17.4
Bender et al 2016 ( Haiti ) -0.1769 [-0.8203; 0.4664] 2.0
Subramanian et al 2014 ( Bangladesh ) 0.0568 [-0.0605; 0.1741] 61.1
Sordillo et al 2017 ( USA(CA_MA_MO) ) 0.7355 [ 0.3600; 1.1109] 6.0
Azad et al 2015 ( Canada ) 0.6149 [ 0.3048; 0.9250] 8.7
%W(random)
Wood et al 2017 ( South Africa ) 14.3
Pannaraj et al 2017 ( USA(CA_FL) ) 20.4
Bender et al 2016 ( Haiti ) 9.1
Subramanian et al 2014 ( Bangladesh ) 23.1
Sordillo et al 2017 ( USA(CA_MA_MO) ) 15.5
Azad et al 2015 ( Canada ) 17.6
Number of studies combined: k = 6
RD 95%-CI z p-value
Fixed effect model 0.1808 [0.0891; 0.2725] 3.87 0.0001
Random effects model 0.2909 [0.0458; 0.5360] 2.33 0.0200
Quantifying heterogeneity:
tau^2 = 0.0640; H = 2.10 [1.41; 3.13]; I^2 = 77.3% [49.6%; 89.8%]
Test of heterogeneity:
Q d.f. p-value
22.05 5 0.0005
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Wood et al 2017 ( South Africa ) | 0.569010986228987 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.0176451947099079 |
| Bender et al 2016 ( Haiti ) | 0.589859305402284 |
| Subramanian et al 2014 ( Bangladesh ) | 0.342537683608756 |
| Sordillo et al 2017 ( USA(CA_MA_MO) ) | 0.000123424504683378 |
| Azad et al 2015 ( Canada ) | 0.000101690866421991 |
RD 95%-CI %W(fixed)
Thompson et al 2015 ( USA(NC) ) 0.8754 [ 0.1366; 1.6142] 1.6
Wood et al 2017 ( South Africa ) 0.1214 [-0.2963; 0.5390] 5.0
Pannaraj et al 2017 ( USA(CA_FL) ) 0.2665 [ 0.0464; 0.4866] 18.2
Bender et al 2016 ( Haiti ) -0.1769 [-0.8203; 0.4664] 2.1
Subramanian et al 2014 ( Bangladesh ) 0.0568 [-0.0605; 0.1741] 63.9
Azad et al 2015 ( Canada ) 0.6149 [ 0.3048; 0.9250] 9.1
%W(random)
Thompson et al 2015 ( USA(NC) ) 7.4
Wood et al 2017 ( South Africa ) 15.0
Pannaraj et al 2017 ( USA(CA_FL) ) 22.8
Bender et al 2016 ( Haiti ) 9.0
Subramanian et al 2014 ( Bangladesh ) 26.7
Azad et al 2015 ( Canada ) 19.0
Number of studies combined: k = 6
RD 95%-CI z p-value
Fixed effect model 0.1574 [0.0636; 0.2512] 3.29 0.0010
Random effects model 0.2602 [0.0267; 0.4936] 2.18 0.0290
Quantifying heterogeneity:
tau^2 = 0.0495; H = 1.83 [1.20; 2.80]; I^2 = 70.3% [30.5%; 87.3%]
Test of heterogeneity:
Q d.f. p-value
16.83 5 0.0048
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Thompson et al 2015 ( USA(NC) ) | 0.0202100021212404 |
| Wood et al 2017 ( South Africa ) | 0.569010986228987 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.0176451947099079 |
| Bender et al 2016 ( Haiti ) | 0.589859305402284 |
| Subramanian et al 2014 ( Bangladesh ) | 0.342537683608756 |
| Azad et al 2015 ( Canada ) | 0.000101690866421991 |
RD 95%-CI %W(fixed)
Azad et al 2015 (Canada) 2.0223 [ 1.0746; 2.9701] 23.9
Bender et al 2016 (Haiti) -0.5119 [-2.7851; 1.7614] 4.1
Pannaraj et al 2017 (USA(CA_FL)) 0.5934 [-0.0958; 1.2826] 45.1
Sordillo et al 2017 (USA(CA_MA_MO)) 1.5749 [ 0.6821; 2.4677] 26.9
%W(random)
Azad et al 2015 (Canada) 27.7
Bender et al 2016 (Haiti) 10.8
Pannaraj et al 2017 (USA(CA_FL)) 32.8
Sordillo et al 2017 (USA(CA_MA_MO)) 28.8
Number of studies combined: k = 4
RD 95%-CI z p-value
Fixed effect model 1.1523 [0.6894; 1.6152] 4.88 < 0.0001
Random effects model 1.1519 [0.2829; 2.0209] 2.60 0.0094
Quantifying heterogeneity:
tau^2 = 0.4763; H = 1.70 [1.00; 2.92]; I^2 = 65.4% [0.0%; 88.2%]
Test of heterogeneity:
Q d.f. p-value
8.68 3 0.0338
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Azad et al 2015 (Canada) | 2.88635033937751e-05 |
| Bender et al 2016 (Haiti) | 0.658981004403214 |
| Pannaraj et al 2017 (USA(CA_FL)) | 0.0914811823311381 |
| Sordillo et al 2017 (USA(CA_MA_MO)) | 0.000545678208685348 |
RD 95%-CI %W(fixed)
Azad et al 2015 (Canada) 0.6820 [-1.3391; 2.7031] 14.4
Bender et al 2016 (Haiti) -0.3508 [-4.3974; 3.6958] 3.6
Pannaraj et al 2017 (USA(CA_FL)) 0.7880 [-0.2996; 1.8755] 49.7
Sordillo et al 2017 (USA(CA_MA_MO)) 1.1977 [-0.1522; 2.5476] 32.3
%W(random)
Azad et al 2015 (Canada) 14.4
Bender et al 2016 (Haiti) 3.6
Pannaraj et al 2017 (USA(CA_FL)) 49.7
Sordillo et al 2017 (USA(CA_MA_MO)) 32.3
Number of studies combined: k = 4
RD 95%-CI z p-value
Fixed effect model 0.8641 [0.0971; 1.6310] 2.21 0.0272
Random effects model 0.8641 [0.0971; 1.6310] 2.21 0.0272
Quantifying heterogeneity:
tau^2 = 0; H = 1.00 [1.00; 1.17]; I^2 = 0.0% [0.0%; 27.2%]
Test of heterogeneity:
Q d.f. p-value
0.63 3 0.8893
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Azad et al 2015 (Canada) | 0.508396867999409 |
| Bender et al 2016 (Haiti) | 0.865079808120753 |
| Pannaraj et al 2017 (USA(CA_FL)) | 0.155598040795797 |
| Sordillo et al 2017 (USA(CA_MA_MO)) | 0.0820319111581724 |
RD 95%-CI %W(fixed)
Subramanian et al 2014 (Bangladesh) 0.0308 [-0.0757; 0.1372] 44.1
Azad et al 2015 (Canada) 0.5818 [ 0.4102; 0.7534] 17.0
Pannaraj et al 2017 (USA(CA_FL)) 0.3161 [ 0.1504; 0.4819] 18.2
Sordillo et al 2017 (USA(CA_MA_MO)) 0.5214 [ 0.3626; 0.6802] 19.8
Thompson et al 2015 (USA(NC)) 0.2911 [-0.4807; 1.0628] 0.8
%W(random)
Subramanian et al 2014 (Bangladesh) 24.0
Azad et al 2015 (Canada) 22.6
Pannaraj et al 2017 (USA(CA_FL)) 22.7
Sordillo et al 2017 (USA(CA_MA_MO)) 22.9
Thompson et al 2015 (USA(NC)) 7.8
Number of studies combined: k = 5
RD 95%-CI z p-value
Fixed effect model 0.2758 [0.2051; 0.3465] 7.64 < 0.0001
Random effects model 0.3526 [0.0926; 0.6125] 2.66 0.0079
Quantifying heterogeneity:
tau^2 = 0.0703; H = 3.24 [2.28; 4.61]; I^2 = 90.5% [80.7%; 95.3%]
Test of heterogeneity:
Q d.f. p-value
41.99 4 < 0.0001
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 (Bangladesh) | 0.570837554151296 |
| Azad et al 2015 (Canada) | 2.9999698377109e-11 |
| Pannaraj et al 2017 (USA(CA_FL)) | 0.000185565976276297 |
| Sordillo et al 2017 (USA(CA_MA_MO)) | 1.24192582145007e-10 |
| Thompson et al 2015 (USA(NC)) | 0.459754398037424 |
With GAMM fit and 95%CI.
Number of infants by duration of bf in the test set
<=2 months >2 months
26 13
Number of samples by duration of bf in the test set
<=2 months >2 months
483 252
Number of samples by duration of bf in the test set (>6 months only)
<=2 months >2 months
305 176
Test for age > 6 months and <15months GAM part
| Estimate | Std. Error | t value | Pr(>|t|) | |
|---|---|---|---|---|
| (Intercept) | 11.516456 | 0.4287802 | 26.858644 | 0.0000000 |
| month.exbf2>2 months | -1.634246 | 0.7401967 | -2.207854 | 0.0280084 |
| edf | Ref.df | F | p-value | |
|---|---|---|---|---|
| s(age.sample):month.exbf2<=2 months | 1.000001 | 1.000001 | 120.79393 | 0 |
| s(age.sample):month.exbf2>2 months | 1.000000 | 1.000000 | 60.88972 | 0 |
LME part
| Value | Std.Error | DF | t-value | p-value | |
|---|---|---|---|---|---|
| X(Intercept) | 11.516456 | 0.4302022 | 264 | 26.769865 | 0.0000000 |
| Xmonth.exbf2>2 months | -1.634246 | 0.7426508 | 37 | -2.200557 | 0.0340874 |
| Xs(age.sample):month.exbf2<=2 monthsFx1 | 2.352653 | 0.2147700 | 264 | 10.954291 | 0.0000000 |
| Xs(age.sample):month.exbf2>2 monthsFx1 | 2.231823 | 0.2869630 | 264 | 7.777391 | 0.0000000 |
With GAMM fit and 95%CI.
Samples <= 6 months only
Samples <=6 months only
Subramanian (Bangladesh) data only.
Shannon index.
For samples <=6 months old only.
RD 95%-CI %W(fixed)
Subramanian et al 2014 ( Bangladesh ) 0.0677 [-0.0136; 0.1491] 79.0
Azad et al 2015 ( Canada ) 0.3752 [ 0.0596; 0.6908] 5.3
Bender et al 2016 ( Haiti ) 0.4922 [-0.3266; 1.3110] 0.8
Wood et al 2017 ( South Africa ) 0.5113 [ 0.0923; 0.9303] 3.0
Pannaraj et al 2017 ( USA(CA_FL) ) 0.1201 [-0.1362; 0.3764] 8.0
Sordillo et al 2017 ( USA(CA_MA_MO) ) 0.6457 [ 0.2430; 1.0485] 3.2
Thompson et al 2015 ( USA(NC) ) 0.4111 [-0.4054; 1.2277] 0.8
%W(random)
Subramanian et al 2014 ( Bangladesh ) 28.0
Azad et al 2015 ( Canada ) 16.8
Bender et al 2016 ( Haiti ) 4.9
Wood et al 2017 ( South Africa ) 12.6
Pannaraj et al 2017 ( USA(CA_FL) ) 19.6
Sordillo et al 2017 ( USA(CA_MA_MO) ) 13.2
Thompson et al 2015 ( USA(NC) ) 4.9
Number of studies combined: k = 7
RD 95%-CI z p-value
Fixed effect model 0.1259 [0.0536; 0.1982] 3.41 0.0006
Random effects model 0.2995 [0.1020; 0.4969] 2.97 0.0030
Quantifying heterogeneity:
tau^2 = 0.0346; H = 1.59 [1.05; 2.41]; I^2 = 60.7% [9.9%; 82.8%]
Test of heterogeneity:
Q d.f. p-value
15.25 6 0.0184
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 ( Bangladesh ) | 0.102847325927163 |
| Azad et al 2015 ( Canada ) | 0.01980051110656 |
| Bender et al 2016 ( Haiti ) | 0.238756122389415 |
| Wood et al 2017 ( South Africa ) | 0.0167677830041401 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.358399385859461 |
| Sordillo et al 2017 ( USA(CA_MA_MO) ) | 0.00167635766494574 |
| Thompson et al 2015 ( USA(NC) ) | 0.32371285335117 |
RD 95%-CI %W(fixed)
Subramanian et al 2014 ( Bangladesh ) 0.0673 [-0.0127; 0.1473] 77.1
Azad et al 2015 ( Canada ) 0.3721 [ 0.0590; 0.6852] 5.0
Bender et al 2016 ( Haiti ) 0.4601 [-0.3413; 1.2616] 0.8
Wood et al 2017 ( South Africa ) 0.4996 [ 0.0848; 0.9143] 2.9
Pannaraj et al 2017 ( USA(CA_FL) ) 0.1447 [-0.0763; 0.3657] 10.1
Sordillo et al 2017 ( USA(CA_MA_MO) ) 0.6461 [ 0.2454; 1.0467] 3.1
Thompson et al 2015 ( USA(NC) ) 0.3555 [-0.3448; 1.0557] 1.0
%W(random)
Subramanian et al 2014 ( Bangladesh ) 28.2
Azad et al 2015 ( Canada ) 16.1
Bender et al 2016 ( Haiti ) 4.5
Wood et al 2017 ( South Africa ) 12.0
Pannaraj et al 2017 ( USA(CA_FL) ) 21.0
Sordillo et al 2017 ( USA(CA_MA_MO) ) 12.5
Thompson et al 2015 ( USA(NC) ) 5.7
Number of studies combined: k = 7
RD 95%-CI z p-value
Fixed effect model 0.1266 [0.0564; 0.1969] 3.53 0.0004
Random effects model 0.2909 [0.1053; 0.4765] 3.07 0.0021
Quantifying heterogeneity:
tau^2 = 0.0301; H = 1.59 [1.05; 2.41]; I^2 = 60.4% [9.1%; 82.7%]
Test of heterogeneity:
Q d.f. p-value
15.14 6 0.0192
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 ( Bangladesh ) | 0.0990100956520888 |
| Azad et al 2015 ( Canada ) | 0.019839103185688 |
| Bender et al 2016 ( Haiti ) | 0.260501865374435 |
| Wood et al 2017 ( South Africa ) | 0.0182288177251842 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.19952096913775 |
| Sordillo et al 2017 ( USA(CA_MA_MO) ) | 0.00157427402976728 |
| Thompson et al 2015 ( USA(NC) ) | 0.319751771051308 |
RD 95%-CI %W(fixed)
Subramanian et al 2014 ( Bangladesh ) 0.0953 [ 0.0196; 0.1710] 80.5
Azad et al 2015 ( Canada ) 0.2877 [-0.0327; 0.6082] 4.5
Bender et al 2016 ( Haiti ) 0.3082 [-0.3766; 0.9931] 1.0
Wood et al 2017 ( South Africa ) 0.4724 [ 0.0489; 0.8958] 2.6
Pannaraj et al 2017 ( USA(CA_FL) ) 0.2168 [ 0.0121; 0.4215] 11.0
Thompson et al 2015 ( USA(NC) ) 0.7261 [-0.2385; 1.6906] 0.5
%W(random)
Subramanian et al 2014 ( Bangladesh ) 52.8
Azad et al 2015 ( Canada ) 12.0
Bender et al 2016 ( Haiti ) 3.1
Wood et al 2017 ( South Africa ) 7.4
Pannaraj et al 2017 ( USA(CA_FL) ) 23.2
Thompson et al 2015 ( USA(NC) ) 1.6
Number of studies combined: k = 6
RD 95%-CI z p-value
Fixed effect model 0.1322 [0.0643; 0.2001] 3.82 0.0001
Random effects model 0.1910 [0.0685; 0.3134] 3.06 0.0022
Quantifying heterogeneity:
tau^2 = 0.0059; H = 1.15 [1.00; 1.78]; I^2 = 25.0% [0.0%; 68.4%]
Test of heterogeneity:
Q d.f. p-value
6.66 5 0.2469
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 ( Bangladesh ) | 0.0136266394489582 |
| Azad et al 2015 ( Canada ) | 0.0784131649118116 |
| Bender et al 2016 ( Haiti ) | 0.377692577417145 |
| Wood et al 2017 ( South Africa ) | 0.0288048675369895 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.0379096968161372 |
| Thompson et al 2015 ( USA(NC) ) | 0.140133230873501 |
RD 95%-CI %W(fixed)
Subramanian et al 2014 ( Bangladesh ) 0.2592 [ 0.1185; 0.3999] 57.3
Azad et al 2015 ( Canada ) 0.3262 [ 0.0159; 0.6365] 11.8
Bender et al 2016 ( Haiti ) -0.1146 [-0.7954; 0.5662] 2.4
Wood et al 2017 ( South Africa ) 0.3071 [-0.1311; 0.7452] 5.9
Pannaraj et al 2017 ( USA(CA_FL) ) 0.3732 [ 0.0808; 0.6657] 13.3
Sordillo et al 2017 ( USA(CA_MA_MO) ) 0.7684 [ 0.3821; 1.1546] 7.6
Thompson et al 2015 ( USA(NC) ) 0.3001 [-0.5308; 1.1310] 1.6
%W(random)
Subramanian et al 2014 ( Bangladesh ) 40.5
Azad et al 2015 ( Canada ) 15.7
Bender et al 2016 ( Haiti ) 4.0
Wood et al 2017 ( South Africa ) 8.9
Pannaraj et al 2017 ( USA(CA_FL) ) 17.2
Sordillo et al 2017 ( USA(CA_MA_MO) ) 11.0
Thompson et al 2015 ( USA(NC) ) 2.7
Number of studies combined: k = 7
RD 95%-CI z p-value
Fixed effect model 0.3153 [0.2088; 0.4219] 5.80 < 0.0001
Random effects model 0.3359 [0.1959; 0.4759] 4.70 < 0.0001
Quantifying heterogeneity:
tau^2 = 0.0074; H = 1.12 [1.00; 1.67]; I^2 = 20.9% [0.0%; 64.3%]
Test of heterogeneity:
Q d.f. p-value
7.59 6 0.2700
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 ( Bangladesh ) | 0.000305463231694058 |
| Azad et al 2015 ( Canada ) | 0.0393559233405728 |
| Bender et al 2016 ( Haiti ) | 0.74142212926805 |
| Wood et al 2017 ( South Africa ) | 0.169568310346119 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.0123688713005407 |
| Sordillo et al 2017 ( USA(CA_MA_MO) ) | 9.65594918082499e-05 |
| Thompson et al 2015 ( USA(NC) ) | 0.479014124949741 |
Show the results of Shannon indexes only.
RD 95%-CI %W(fixed)
Subramanian et al 2014 ( Bangladesh ) 0.2592 [ 0.1185; 0.3999] 58.8
Azad et al 2015 ( Canada ) 0.3262 [ 0.0159; 0.6365] 12.1
Wood et al 2017 ( South Africa ) 0.3071 [-0.1311; 0.7452] 6.1
Pannaraj et al 2017 ( USA(CA_FL) ) 0.3732 [ 0.0808; 0.6657] 13.6
Sordillo et al 2017 ( USA(CA_MA_MO) ) 0.7684 [ 0.3821; 1.1546] 7.8
Thompson et al 2015 ( USA(NC) ) 0.3001 [-0.5308; 1.1310] 1.7
%W(random)
Subramanian et al 2014 ( Bangladesh ) 45.8
Azad et al 2015 ( Canada ) 15.5
Wood et al 2017 ( South Africa ) 8.5
Pannaraj et al 2017 ( USA(CA_FL) ) 17.1
Sordillo et al 2017 ( USA(CA_MA_MO) ) 10.6
Thompson et al 2015 ( USA(NC) ) 2.5
Number of studies combined: k = 6
RD 95%-CI z p-value
Fixed effect model 0.3261 [0.2183; 0.4340] 5.93 < 0.0001
Random effects model 0.3483 [0.2145; 0.4821] 5.10 < 0.0001
Quantifying heterogeneity:
tau^2 = 0.0050; H = 1.10 [1.00; 1.61]; I^2 = 16.9% [0.0%; 61.6%]
Test of heterogeneity:
Q d.f. p-value
6.02 5 0.3047
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 ( Bangladesh ) | 0.000305463231694058 |
| Azad et al 2015 ( Canada ) | 0.0393559233405728 |
| Wood et al 2017 ( South Africa ) | 0.169568310346119 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.0123688713005407 |
| Sordillo et al 2017 ( USA(CA_MA_MO) ) | 9.65594918082499e-05 |
| Thompson et al 2015 ( USA(NC) ) | 0.479014124949741 |
RD 95%-CI %W(fixed)
Subramanian et al 2014 ( Bangladesh ) 0.2592 [ 0.1185; 0.3999] 58.3
Azad et al 2015 ( Canada ) 0.3262 [ 0.0159; 0.6365] 12.0
Bender et al 2016 ( Haiti ) -0.1146 [-0.7954; 0.5662] 2.5
Wood et al 2017 ( South Africa ) 0.3071 [-0.1311; 0.7452] 6.0
Pannaraj et al 2017 ( USA(CA_FL) ) 0.3732 [ 0.0808; 0.6657] 13.5
Sordillo et al 2017 ( USA(CA_MA_MO) ) 0.7684 [ 0.3821; 1.1546] 7.7
%W(random)
Subramanian et al 2014 ( Bangladesh ) 36.5
Azad et al 2015 ( Canada ) 17.2
Bender et al 2016 ( Haiti ) 4.9
Wood et al 2017 ( South Africa ) 10.3
Pannaraj et al 2017 ( USA(CA_FL) ) 18.6
Sordillo et al 2017 ( USA(CA_MA_MO) ) 12.6
Number of studies combined: k = 6
RD 95%-CI z p-value
Fixed effect model 0.3156 [0.2082; 0.4230] 5.76 < 0.0001
Random effects model 0.3427 [0.1851; 0.5004] 4.26 < 0.0001
Quantifying heterogeneity:
tau^2 = 0.0126; H = 1.23 [1.00; 1.94]; I^2 = 34.1% [0.0%; 73.5%]
Test of heterogeneity:
Q d.f. p-value
7.58 5 0.1807
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 ( Bangladesh ) | 0.000305463231694058 |
| Azad et al 2015 ( Canada ) | 0.0393559233405728 |
| Bender et al 2016 ( Haiti ) | 0.74142212926805 |
| Wood et al 2017 ( South Africa ) | 0.169568310346119 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.0123688713005407 |
| Sordillo et al 2017 ( USA(CA_MA_MO) ) | 9.65594918082499e-05 |
RD 95%-CI %W(fixed)
Subramanian et al 2014 ( Bangladesh ) 0.2592 [ 0.1185; 0.3999] 62.0
Azad et al 2015 ( Canada ) 0.3262 [ 0.0159; 0.6365] 12.8
Bender et al 2016 ( Haiti ) -0.1146 [-0.7954; 0.5662] 2.7
Wood et al 2017 ( South Africa ) 0.3071 [-0.1311; 0.7452] 6.4
Pannaraj et al 2017 ( USA(CA_FL) ) 0.3732 [ 0.0808; 0.6657] 14.4
Thompson et al 2015 ( USA(NC) ) 0.3001 [-0.5308; 1.1310] 1.8
%W(random)
Subramanian et al 2014 ( Bangladesh ) 62.0
Azad et al 2015 ( Canada ) 12.8
Bender et al 2016 ( Haiti ) 2.7
Wood et al 2017 ( South Africa ) 6.4
Pannaraj et al 2017 ( USA(CA_FL) ) 14.4
Thompson et al 2015 ( USA(NC) ) 1.8
Number of studies combined: k = 6
RD 95%-CI z p-value
Fixed effect model 0.2780 [0.1672; 0.3889] 4.92 < 0.0001
Random effects model 0.2780 [0.1672; 0.3889] 4.92 < 0.0001
Quantifying heterogeneity:
tau^2 = 0; H = 1.00 [1.00; 1.21]; I^2 = 0.0% [0.0%; 32.0%]
Test of heterogeneity:
Q d.f. p-value
1.87 5 0.8674
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 ( Bangladesh ) | 0.000305463231694058 |
| Azad et al 2015 ( Canada ) | 0.0393559233405728 |
| Bender et al 2016 ( Haiti ) | 0.74142212926805 |
| Wood et al 2017 ( South Africa ) | 0.169568310346119 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.0123688713005407 |
| Thompson et al 2015 ( USA(NC) ) | 0.479014124949741 |
Show results of Shannon index only.
RD 95%-CI %W(fixed)
Azad et al 2015 (Canada) 0.1424 [-0.0984; 0.3832] 40.8
Bender et al 2016 (Haiti) -0.2018 [-0.9752; 0.5715] 4.0
Pannaraj et al 2017 (USA(CA_FL)) 0.3734 [ 0.1294; 0.6174] 39.7
Sordillo et al 2017 (USA(CA_MA_MO)) 0.4321 [ 0.0420; 0.8223] 15.5
%W(random)
Azad et al 2015 (Canada) 38.3
Bender et al 2016 (Haiti) 5.4
Pannaraj et al 2017 (USA(CA_FL)) 37.6
Sordillo et al 2017 (USA(CA_MA_MO)) 18.6
Number of studies combined: k = 4
RD 95%-CI z p-value
Fixed effect model 0.2656 [0.1118; 0.4194] 3.38 0.0007
Random effects model 0.2647 [0.0798; 0.4495] 2.81 0.0050
Quantifying heterogeneity:
tau^2 = 0.0081; H = 1.13 [1.00; 2.90]; I^2 = 22.3% [0.0%; 88.1%]
Test of heterogeneity:
Q d.f. p-value
3.86 3 0.2771
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Azad et al 2015 (Canada) | 0.246532761397953 |
| Bender et al 2016 (Haiti) | 0.608996225108868 |
| Pannaraj et al 2017 (USA(CA_FL)) | 0.00270151112577258 |
| Sordillo et al 2017 (USA(CA_MA_MO)) | 0.0299341350698865 |
RD 95%-CI %W(fixed)
Azad et al 2015 (Canada) 0.4873 [ 0.0230; 0.9515] 40.3
Pannaraj et al 2017 (USA(CA_FL)) -0.0737 [-0.5869; 0.4395] 33.0
Sordillo et al 2017 (USA(CA_MA_MO)) 1.0833 [ 0.5127; 1.6540] 26.7
%W(random)
Azad et al 2015 (Canada) 34.9
Pannaraj et al 2017 (USA(CA_FL)) 33.4
Sordillo et al 2017 (USA(CA_MA_MO)) 31.7
Number of studies combined: k = 3
RD 95%-CI z p-value
Fixed effect model 0.4612 [ 0.1665; 0.7560] 3.07 0.0022
Random effects model 0.4888 [-0.1327; 1.1103] 1.54 0.1232
Quantifying heterogeneity:
tau^2 = 0.2323; H = 2.09 [1.16; 3.77]; I^2 = 77.1% [25.6%; 93.0%]
Test of heterogeneity:
Q d.f. p-value
8.75 2 0.0126
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Azad et al 2015 (Canada) | 0.0396622679428872 |
| Pannaraj et al 2017 (USA(CA_FL)) | 0.778417002121859 |
| Sordillo et al 2017 (USA(CA_MA_MO)) | 0.000198560001433614 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| shannon | 0.3359260 | 0.0714283 | 0.1959290 | 0.4759229 | 4.702980 | 0.0000026 | 0.0000103 |
| observed_species | 0.2908894 | 0.0946918 | 0.1052969 | 0.4764819 | 3.071960 | 0.0021266 | 0.0029552 |
| pd_whole_tree | 0.1909514 | 0.0624970 | 0.0684595 | 0.3134432 | 3.055369 | 0.0022478 | 0.0029552 |
| chao1 | 0.2994547 | 0.1007464 | 0.1019953 | 0.4969141 | 2.972360 | 0.0029552 | 0.0029552 |
RD 95%-CI %W(fixed)
Subramanian et al 2014 ( Bangladesh ) 0.0550 [-0.0189; 0.1289] 65.2
Azad et al 2015 ( Canada ) 0.5725 [ 0.3986; 0.7464] 11.8
Bender et al 2016 ( Haiti ) NA 0.0
Wood et al 2017 ( South Africa ) NA 0.0
Pannaraj et al 2017 ( USA(CA_FL) ) 0.1302 [-0.0599; 0.3202] 9.9
Sordillo et al 2017 ( USA(CA_MA_MO) ) 0.4245 [ 0.2553; 0.5937] 12.4
Thompson et al 2015 ( USA(NC) ) 0.4233 [-0.2687; 1.1153] 0.7
%W(random)
Subramanian et al 2014 ( Bangladesh ) 24.7
Azad et al 2015 ( Canada ) 22.4
Bender et al 2016 ( Haiti ) 0.0
Wood et al 2017 ( South Africa ) 0.0
Pannaraj et al 2017 ( USA(CA_FL) ) 21.9
Sordillo et al 2017 ( USA(CA_MA_MO) ) 22.6
Thompson et al 2015 ( USA(NC) ) 8.3
Number of studies combined: k = 5
RD 95%-CI z p-value
Fixed effect model 0.1720 [0.1123; 0.2316] 5.65 < 0.0001
Random effects model 0.3016 [0.0580; 0.5451] 2.43 0.0152
Quantifying heterogeneity:
tau^2 = 0.0610; H = 3.13 [2.19; 4.49]; I^2 = 89.8% [79.1%; 95.0%]
Test of heterogeneity:
Q d.f. p-value
39.26 4 < 0.0001
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 ( Bangladesh ) | 0.144460866036347 |
| Azad et al 2015 ( Canada ) | 1.0991009354299e-10 |
| Bender et al 2016 ( Haiti ) | NA |
| Wood et al 2017 ( South Africa ) | NA |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.179455833167877 |
| Sordillo et al 2017 ( USA(CA_MA_MO) ) | 8.77670396356771e-07 |
| Thompson et al 2015 ( USA(NC) ) | 0.230600549600578 |
RD 95%-CI %W(fixed)
Subramanian et al 2014 ( Bangladesh ) 0.0603 [-0.0124; 0.1329] 63.5
Azad et al 2015 ( Canada ) 0.5895 [ 0.4168; 0.7623] 11.2
Bender et al 2016 ( Haiti ) NA 0.0
Wood et al 2017 ( South Africa ) NA 0.0
Pannaraj et al 2017 ( USA(CA_FL) ) 0.1163 [-0.0479; 0.2806] 12.4
Sordillo et al 2017 ( USA(CA_MA_MO) ) 0.4610 [ 0.2928; 0.6291] 11.9
Thompson et al 2015 ( USA(NC) ) 0.3661 [-0.2275; 0.9598] 1.0
%W(random)
Subramanian et al 2014 ( Bangladesh ) 24.1
Azad et al 2015 ( Canada ) 21.9
Bender et al 2016 ( Haiti ) 0.0
Wood et al 2017 ( South Africa ) 0.0
Pannaraj et al 2017 ( USA(CA_FL) ) 22.1
Sordillo et al 2017 ( USA(CA_MA_MO) ) 22.0
Thompson et al 2015 ( USA(NC) ) 10.0
Number of studies combined: k = 5
RD 95%-CI z p-value
Fixed effect model 0.1772 [0.1192; 0.2351] 6.00 < 0.0001
Random effects model 0.3070 [0.0641; 0.5500] 2.48 0.0133
Quantifying heterogeneity:
tau^2 = 0.0625; H = 3.30 [2.33; 4.69]; I^2 = 90.8% [81.6%; 95.4%]
Test of heterogeneity:
Q d.f. p-value
43.68 4 < 0.0001
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 ( Bangladesh ) | 0.104033167825551 |
| Azad et al 2015 ( Canada ) | 2.26960893212611e-11 |
| Bender et al 2016 ( Haiti ) | NA |
| Wood et al 2017 ( South Africa ) | NA |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.165000455562882 |
| Sordillo et al 2017 ( USA(CA_MA_MO) ) | 7.73447284594136e-08 |
| Thompson et al 2015 ( USA(NC) ) | 0.226684364502839 |
RD 95%-CI %W(fixed)
Subramanian et al 2014 ( Bangladesh ) 0.0646 [-0.0047; 0.1338] 72.9
Azad et al 2015 ( Canada ) 0.5311 [ 0.3540; 0.7082] 11.2
Bender et al 2016 ( Haiti ) NA 0.0
Wood et al 2017 ( South Africa ) NA 0.0
Pannaraj et al 2017 ( USA(CA_FL) ) 0.2032 [ 0.0523; 0.3541] 15.4
Thompson et al 2015 ( USA(NC) ) 0.8566 [ 0.0509; 1.6623] 0.5
%W(random)
Subramanian et al 2014 ( Bangladesh ) 32.9
Azad et al 2015 ( Canada ) 29.1
Bender et al 2016 ( Haiti ) 0.0
Wood et al 2017 ( South Africa ) 0.0
Pannaraj et al 2017 ( USA(CA_FL) ) 30.2
Thompson et al 2015 ( USA(NC) ) 7.8
Number of studies combined: k = 4
RD 95%-CI z p-value
Fixed effect model 0.1422 [0.0830; 0.2013] 4.71 < 0.0001
Random effects model 0.3037 [0.0475; 0.5598] 2.32 0.0202
Quantifying heterogeneity:
tau^2 = 0.0506; H = 3.00 [1.97; 4.57]; I^2 = 88.9% [74.2%; 95.2%]
Test of heterogeneity:
Q d.f. p-value
26.99 3 < 0.0001
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 ( Bangladesh ) | 0.0676383461236607 |
| Azad et al 2015 ( Canada ) | 4.17049539317814e-09 |
| Bender et al 2016 ( Haiti ) | NA |
| Wood et al 2017 ( South Africa ) | NA |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.00831447939658577 |
| Thompson et al 2015 ( USA(NC) ) | 0.0371791605971582 |
RD 95%-CI %W(fixed)
Subramanian et al 2014 ( Bangladesh ) 0.2131 [ 0.0843; 0.3420] 39.0
Azad et al 2015 ( Canada ) 0.5872 [ 0.4153; 0.7590] 21.9
Pannaraj et al 2017 ( USA(CA_FL) ) 0.2570 [ 0.0375; 0.4765] 13.5
Sordillo et al 2017 ( USA(CA_MA_MO) ) 0.5660 [ 0.4038; 0.7282] 24.6
Thompson et al 2015 ( USA(NC) ) -0.0180 [-0.8408; 0.8049] 1.0
%W(random)
Subramanian et al 2014 ( Bangladesh ) 25.8
Azad et al 2015 ( Canada ) 23.8
Pannaraj et al 2017 ( USA(CA_FL) ) 21.4
Sordillo et al 2017 ( USA(CA_MA_MO) ) 24.2
Thompson et al 2015 ( USA(NC) ) 4.8
Number of studies combined: k = 5
RD 95%-CI z p-value
Fixed effect model 0.3858 [0.3053; 0.4663] 9.39 < 0.0001
Random effects model 0.3857 [0.1872; 0.5843] 3.81 0.0001
Quantifying heterogeneity:
tau^2 = 0.0355; H = 2.19 [1.42; 3.37]; I^2 = 79.1% [50.4%; 91.2%]
Test of heterogeneity:
Q d.f. p-value
19.16 4 0.0007
Details on meta-analytical method:
- Inverse variance method
- DerSimonian-Laird estimator for tau^2
| study | pval |
|---|---|
| Subramanian et al 2014 ( Bangladesh ) | 0.00119013497616748 |
| Azad et al 2015 ( Canada ) | 2.14964602978342e-11 |
| Pannaraj et al 2017 ( USA(CA_FL) ) | 0.0217486284946625 |
| Sordillo et al 2017 ( USA(CA_MA_MO) ) | 7.9318409863511e-12 |
| Thompson et al 2015 ( USA(NC) ) | 0.965887658685873 |
| estimate.conbf | se.conbf | ll.conbf | ul.conbf | z.conbf | p.conbf | p.adjust.conbf | |
|---|---|---|---|---|---|---|---|
| shannon | 0.3857475 | 0.1012964 | 0.1872101 | 0.5842849 | 3.808105 | 0.0001400 | 0.0005601 |
| observed_species | 0.3070476 | 0.1239712 | 0.0640686 | 0.5500267 | 2.476766 | 0.0132579 | 0.0201585 |
| pd_whole_tree | 0.3036608 | 0.1306976 | 0.0474982 | 0.5598233 | 2.323384 | 0.0201585 | 0.0201585 |
| chao1 | 0.3015700 | 0.1242513 | 0.0580420 | 0.5450980 | 2.427098 | 0.0152201 | 0.0201585 |
Results of 7 studies.
For samples <= 6 months old only in all studies (note for USA(NC) study: GAMLSS BEZI with random subject effect could not run on very small sample size=> did not include subject random effect). Results of random meta-analysis models for taxa available in at least >50% of studies based on adjusted estimates and standard errors from GAMLSS models with zero-inflated beta family adjusted for infant age at sample collection.
GAMLSS models with zero-inflated beta family
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes | 0.2477163 | 0.0684909 | 0.1134765 | 0.3819560 | 3.616776 | 0.0002983 | 0.0017898 |
| k__bacteria.p__bacteroidetes | 0.2079683 | 0.0756683 | 0.0596613 | 0.3562754 | 2.748422 | 0.0059883 | 0.0179648 |
Nice plot
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales | 0.3015251 | 0.0904382 | 0.1242695 | 0.4787808 | 3.334046 | 0.0008559 | 0.0105564 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales | 0.2100511 | 0.0757620 | 0.0615603 | 0.3585419 | 2.772512 | 0.0055625 | 0.0369277 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales | 0.2005008 | 0.0896354 | 0.0248186 | 0.3761830 | 2.236847 | 0.0252963 | 0.1169955 |
Nice plot
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae | 0.2311548 | 0.0856673 | 0.0632499 | 0.3990596 | 2.698284 | 0.0069698 | 0.0756721 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales.f__bacteroidaceae | 0.2107748 | 0.0807013 | 0.0526031 | 0.3689465 | 2.611789 | 0.0090070 | 0.0855663 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae | 0.2005008 | 0.0896354 | 0.0248186 | 0.3761830 | 2.236847 | 0.0252963 | 0.1747746 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__clostridiaceae | 0.1652266 | 0.0841374 | 0.0003203 | 0.3301328 | 1.963771 | 0.0495566 | 0.3086619 |
Nice plot
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae.g__.eubacterium. | 0.3926058 | 0.1237182 | 0.1501225 | 0.6350890 | 3.173387 | 0.0015067 | 0.0561251 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae.g__megasphaera | 0.4000827 | 0.1416041 | 0.1225438 | 0.6776217 | 2.825361 | 0.0047227 | 0.1115318 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales.f__bacteroidaceae.g__bacteroides | 0.2107748 | 0.0807013 | 0.0526031 | 0.3689465 | 2.611789 | 0.0090070 | 0.1220036 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__clostridium | 0.3454360 | 0.1505929 | 0.0502793 | 0.6405927 | 2.293839 | 0.0217997 | 0.2512768 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae.g__veillonella | 0.2136555 | 0.1033136 | 0.0111645 | 0.4161465 | 2.068028 | 0.0386374 | 0.3598107 |
Nice plot
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes | 0.2469023 | 0.0691970 | 0.1112786 | 0.3825259 | 3.568106 | 0.0003596 | 0.0025170 |
| k__bacteria.p__bacteroidetes | 0.1932696 | 0.0763734 | 0.0435804 | 0.3429588 | 2.530586 | 0.0113872 | 0.0398552 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales | 0.2819748 | 0.0889258 | 0.1076835 | 0.4562662 | 3.170900 | 0.0015197 | 0.0233017 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales | 0.1953538 | 0.0764693 | 0.0454767 | 0.3452308 | 2.554669 | 0.0106289 | 0.0873019 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales | 0.1990864 | 0.0908867 | 0.0209516 | 0.3772211 | 2.190489 | 0.0284888 | 0.1638107 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales.f__bacteroidaceae | 0.1947860 | 0.0815355 | 0.0349794 | 0.3545925 | 2.388972 | 0.0168956 | 0.2092121 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae | 0.2232183 | 0.0940439 | 0.0388955 | 0.4075410 | 2.373553 | 0.0176179 | 0.2092121 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae | 0.1990864 | 0.0908867 | 0.0209516 | 0.3772211 | 2.190489 | 0.0284888 | 0.2460398 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae.g__.eubacterium. | 0.3970460 | 0.1275892 | 0.1469758 | 0.6471162 | 3.111909 | 0.0018588 | 0.0887585 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae.g__megasphaera | 0.4000827 | 0.1416041 | 0.1225438 | 0.6776217 | 2.825361 | 0.0047227 | 0.1804084 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__clostridiaceae.g__ | 0.2425407 | 0.0943469 | 0.0576242 | 0.4274571 | 2.570734 | 0.0101483 | 0.2416618 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales.f__bacteroidaceae.g__bacteroides | 0.1947860 | 0.0815355 | 0.0349794 | 0.3545925 | 2.388972 | 0.0168956 | 0.2804176 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__clostridium | 0.3454360 | 0.1505929 | 0.0502793 | 0.6405927 | 2.293839 | 0.0217997 | 0.3202883 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes | 0.2585644 | 0.0699441 | 0.1214765 | 0.3956523 | 3.696729 | 0.0002184 | 0.0013104 |
| k__bacteria.p__bacteroidetes | 0.2137713 | 0.0769990 | 0.0628560 | 0.3646866 | 2.776286 | 0.0054984 | 0.0164951 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales | 0.3197985 | 0.0708228 | 0.1809883 | 0.4586087 | 4.515471 | 0.0000063 | 0.0001200 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales | 0.2201357 | 0.0770481 | 0.0691242 | 0.3711471 | 2.857121 | 0.0042750 | 0.0324902 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales | 0.1839766 | 0.0915095 | 0.0046213 | 0.3633320 | 2.010465 | 0.0443820 | 0.2108145 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales.f__bacteroidaceae | 0.2061111 | 0.0822865 | 0.0448325 | 0.3673898 | 2.504798 | 0.0122521 | 0.1347734 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae | 0.2060989 | 0.0969374 | 0.0161050 | 0.3960927 | 2.126103 | 0.0334947 | 0.2946724 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae | 0.1839766 | 0.0915095 | 0.0046213 | 0.3633320 | 2.010465 | 0.0443820 | 0.2946724 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__clostridiaceae | 0.1733438 | 0.0868412 | 0.0031382 | 0.3435495 | 1.996101 | 0.0459230 | 0.2946724 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae.g__megasphaera | 0.4521725 | 0.1519683 | 0.1543202 | 0.7500249 | 2.975441 | 0.0029257 | 0.1062738 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae.g__.eubacterium. | 0.3594531 | 0.1297330 | 0.1051810 | 0.6137251 | 2.770714 | 0.0055934 | 0.1062738 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales.f__bacteroidaceae.g__bacteroides | 0.2061111 | 0.0822865 | 0.0448325 | 0.3673898 | 2.504798 | 0.0122521 | 0.1862323 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__clostridium | 0.3557799 | 0.1521514 | 0.0575687 | 0.6539911 | 2.338328 | 0.0193702 | 0.2676612 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__coprococcus | 0.5201042 | 0.2401244 | 0.0494691 | 0.9907393 | 2.165979 | 0.0303128 | 0.3839625 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__clostridiaceae.g__ | 0.5344090 | 0.2586130 | 0.0275369 | 1.0412811 | 2.066443 | 0.0387867 | 0.3877940 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__bacteroidetes | 0.2312551 | 0.0810268 | 0.0724455 | 0.3900646 | 2.854058 | 0.0043165 | 0.0250675 |
| k__bacteria.p__firmicutes | 0.2006141 | 0.0745996 | 0.0544015 | 0.3468267 | 2.689210 | 0.0071621 | 0.0250675 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales | 0.2337644 | 0.0811408 | 0.0747312 | 0.3927975 | 2.880970 | 0.0039645 | 0.0549097 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales | 0.2968923 | 0.1099207 | 0.0814516 | 0.5123329 | 2.700967 | 0.0069138 | 0.0549097 |
| k__bacteria.p__actinobacteria.c__actinobacteria.o__actinomycetales | -0.1557879 | 0.0644216 | -0.2820518 | -0.0295239 | -2.418256 | 0.0155951 | 0.1024820 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales | 0.2117009 | 0.0993562 | 0.0169663 | 0.4064356 | 2.130727 | 0.0331117 | 0.1692374 |
| k__bacteria.p__firmicutes.c__bacilli.o__bacillales | -0.2108602 | 0.1040509 | -0.4147961 | -0.0069242 | -2.026511 | 0.0427125 | 0.1964774 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae | 0.2996094 | 0.0741081 | 0.1543601 | 0.4448586 | 4.042869 | 0.0000528 | 0.0050161 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales.f__bacteroidaceae | 0.2375149 | 0.0870795 | 0.0668422 | 0.4081877 | 2.727563 | 0.0063804 | 0.0850503 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae | 0.2117009 | 0.0993562 | 0.0169663 | 0.4064356 | 2.130727 | 0.0331117 | 0.2621341 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae.g__acidaminococcus | 2.0640609 | 0.5761745 | 0.9347797 | 3.1933421 | 3.582354 | 0.0003405 | 0.0306461 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae.g__.eubacterium. | 0.4120255 | 0.1362642 | 0.1449526 | 0.6790984 | 3.023725 | 0.0024968 | 0.1074319 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae.g__megasphaera | 0.4531996 | 0.1618768 | 0.1359269 | 0.7704723 | 2.799657 | 0.0051157 | 0.1074319 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales.f__bacteroidaceae.g__bacteroides | 0.2375149 | 0.0870795 | 0.0668422 | 0.4081877 | 2.727563 | 0.0063804 | 0.1074319 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae.g__veillonella | 0.2611018 | 0.1085724 | 0.0483038 | 0.4738997 | 2.404864 | 0.0161785 | 0.2080092 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__clostridium | 0.3454360 | 0.1505929 | 0.0502793 | 0.6405927 | 2.293839 | 0.0217997 | 0.2615967 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__coprococcus | 0.5470330 | 0.2571987 | 0.0429329 | 1.0511331 | 2.126889 | 0.0334293 | 0.3166986 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__proteobacteria | -0.3069577 | 0.1017253 | -0.5063356 | -0.1075798 | -3.017517 | 0.0025486 | 0.0178399 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__enterobacteriales | -0.2990541 | 0.1074593 | -0.5096705 | -0.0884377 | -2.782951 | 0.0053867 | 0.1158139 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales | 0.2827724 | 0.1232153 | 0.0412747 | 0.5242700 | 2.294944 | 0.0217363 | 0.2336654 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__bacilli.o__bacillales.f__staphylococcaceae | -0.3327091 | 0.1174047 | -0.5628181 | -0.1026001 | -2.833865 | 0.0045989 | 0.1157163 |
| k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__enterobacteriales.f__enterobacteriaceae | -0.2990541 | 0.1074593 | -0.5096705 | -0.0884377 | -2.782951 | 0.0053867 | 0.1157163 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales.f__bacteroidaceae | 0.3016820 | 0.1105580 | 0.0849923 | 0.5183717 | 2.728721 | 0.0063580 | 0.1157163 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__eubacteriaceae | 0.8045605 | 0.3139899 | 0.1891515 | 1.4199695 | 2.562377 | 0.0103958 | 0.1576704 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae | 0.2827724 | 0.1232153 | 0.0412747 | 0.5242700 | 2.294944 | 0.0217363 | 0.2197783 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae.g__acidaminococcus | 3.3685160 | 0.4300060 | 2.5257196 | 4.2113123 | 7.833648 | 0.0000000 | 0.0000000 |
| k__bacteria.p__firmicutes.c__bacilli.o__bacillales.f__staphylococcaceae.g__staphylococcus | -0.3330596 | 0.1174105 | -0.5631799 | -0.1029393 | -2.836711 | 0.0045581 | 0.1176238 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__eubacteriaceae.g__pseudoramibacter_eubacterium | 0.8762232 | 0.3157991 | 0.2572683 | 1.4951780 | 2.774622 | 0.0055266 | 0.1176238 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__ | 0.3180415 | 0.1163513 | 0.0899972 | 0.5460858 | 2.733460 | 0.0062673 | 0.1176238 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales.f__bacteroidaceae.g__bacteroides | 0.3016820 | 0.1105580 | 0.0849923 | 0.5183717 | 2.728721 | 0.0063580 | 0.1176238 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae.g__.eubacterium. | 0.5384916 | 0.2026827 | 0.1412408 | 0.9357425 | 2.656820 | 0.0078881 | 0.1326643 |
| k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__enterobacteriales.f__enterobacteriaceae.g__ | -0.2862286 | 0.1148106 | -0.5112532 | -0.0612040 | -2.493051 | 0.0126651 | 0.1802335 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__clostridiaceae.g__ | 0.3027671 | 0.1238937 | 0.0599398 | 0.5455944 | 2.443764 | 0.0145349 | 0.1920686 |
| k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__pasteurellales.f__pasteurellaceae.g__aggregatibacter | 0.5722694 | 0.2477375 | 0.0867128 | 1.0578260 | 2.309983 | 0.0208891 | 0.2234010 |
| k__bacteria.p__firmicutes.c__bacilli.o__lactobacillales.f__streptococcaceae.g__lactococcus | 0.5835624 | 0.2676966 | 0.0588868 | 1.1082381 | 2.179940 | 0.0292619 | 0.2849187 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__blautia | 0.3639237 | 0.1848815 | 0.0015626 | 0.7262849 | 1.968416 | 0.0490202 | 0.4534368 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__proteobacteria | -0.719666 | 0.1708821 | -1.054589 | -0.3847433 | -4.211478 | 2.54e-05 | 0.0001522 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__enterobacteriales | -0.5794373 | 0.2324176 | -1.034968 | -0.1239071 | -2.493087 | 0.0126638 | 0.1561867 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__enterobacteriales.f__enterobacteriaceae | -0.5794373 | 0.2324176 | -1.034968 | -0.1239071 | -2.493087 | 0.0126638 | 0.2596077 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__enterobacteriales.f__enterobacteriaceae.g__proteus | -0.2578897 | 0.0008395 | -0.2595351 | -0.2562442 | -307.189026 | 0.0000000 | 0.0000000 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__ruminococcaceae.g__anaerotruncus | -2.9244379 | 0.7060795 | -4.3083283 | -1.5405475 | -4.141797 | 0.0000345 | 0.0018723 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__veillonellaceae.g__phascolarctobacterium | -1.8840686 | 0.8567398 | -3.5632478 | -0.2048894 | -2.199114 | 0.0278698 | 0.6489685 |
| k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__enterobacteriales.f__enterobacteriaceae.g__ | -0.5225859 | 0.2608359 | -1.0338148 | -0.0113570 | -2.003505 | 0.0451232 | 0.9153914 |
Significant (pooled p<0.05) only
| estimate.conbf | se.conbf | ll.conbf | ul.conbf | z.conbf | p.conbf | p.adjust.conbf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes | 0.2891066 | 0.0810164 | 0.1303173 | 0.4478959 | 3.568494 | 0.0003590 | 0.0021542 |
| k__bacteria.p__verrucomicrobia | 0.1902821 | 0.0798894 | 0.0337017 | 0.3468625 | 2.381818 | 0.0172274 | 0.0516822 |
| k__bacteria.p__bacteroidetes | 0.2156141 | 0.0979174 | 0.0236994 | 0.4075287 | 2.201999 | 0.0276654 | 0.0553308 |
Significant only
| estimate.conbf | se.conbf | ll.conbf | ul.conbf | z.conbf | p.conbf | p.adjust.conbf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales | 0.3924806 | 0.0632438 | 0.2685252 | 0.5164361 | 6.205840 | 0.0000000 | 0.0000000 |
| k__bacteria.p__actinobacteria.c__coriobacteriia.o__coriobacteriales | 0.3158688 | 0.0545196 | 0.2090123 | 0.4227252 | 5.793673 | 0.0000000 | 0.0000001 |
| k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__pasteurellales | -0.2179258 | 0.0645356 | -0.3444131 | -0.0914384 | -3.376832 | 0.0007333 | 0.0045218 |
| k__bacteria.p__firmicutes.c__bacilli.o__bacillales | -0.1731560 | 0.0523488 | -0.2757578 | -0.0705541 | -3.307732 | 0.0009405 | 0.0049715 |
| k__bacteria.p__verrucomicrobia.c__verrucomicrobiae.o__verrucomicrobiales | 0.1902859 | 0.0798894 | 0.0337055 | 0.3468662 | 2.381865 | 0.0172252 | 0.0637414 |
| k__bacteria.p__bacteroidetes.c__bacteroidia.o__bacteroidales | 0.2299773 | 0.1084234 | 0.0174714 | 0.4424833 | 2.121104 | 0.0339130 | 0.0965217 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales | 0.1976105 | 0.0958110 | 0.0098243 | 0.3853966 | 2.062503 | 0.0391599 | 0.0965944 |
Significant only
| estimate.conbf | se.conbf | ll.conbf | ul.conbf | z.conbf | p.conbf | p.adjust.conbf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__actinobacteria.c__coriobacteriia.o__coriobacteriales.f__coriobacteriaceae | 0.3158688 | 0.0545196 | 0.2090123 | 0.4227252 | 5.793673 | 0.0000000 | 0.0000001 |
| k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__pasteurellales.f__pasteurellaceae | -0.2179258 | 0.0645356 | -0.3444131 | -0.0914384 | -3.376832 | 0.0007333 | 0.0069659 |
| k__bacteria.p__firmicutes.c__bacilli.o__bacillales.f__staphylococcaceae | -0.1841218 | 0.0598847 | -0.3014937 | -0.0667498 | -3.074603 | 0.0021078 | 0.0160195 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__peptostreptococcaceae | 0.1890903 | 0.0716934 | 0.0485738 | 0.3296068 | 2.637485 | 0.0083523 | 0.0577070 |
| k__bacteria.p__verrucomicrobia.c__verrucomicrobiae.o__verrucomicrobiales.f__verrucomicrobiaceae | 0.1902859 | 0.0798894 | 0.0337055 | 0.3468662 | 2.381865 | 0.0172252 | 0.0872855 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__ruminococcaceae | 0.2044635 | 0.0874835 | 0.0329990 | 0.3759280 | 2.337166 | 0.0194305 | 0.0922951 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__clostridiaceae | 0.1418926 | 0.0667077 | 0.0111478 | 0.2726374 | 2.127078 | 0.0334136 | 0.1233860 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae | 0.3387166 | 0.1598501 | 0.0254162 | 0.6520170 | 2.118964 | 0.0340935 | 0.1233860 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae | 0.1976105 | 0.0958110 | 0.0098243 | 0.3853966 | 2.062503 | 0.0391599 | 0.1240064 |
Significant only
| estimate.conbf | se.conbf | ll.conbf | ul.conbf | z.conbf | p.conbf | p.adjust.conbf | |
|---|---|---|---|---|---|---|---|
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__coprococcus | 0.3299376 | 0.0063390 | 0.3175133 | 0.3423619 | 52.048471 | 0.0000000 | 0.0000000 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__blautia | 0.3815612 | 0.0668433 | 0.2505508 | 0.5125716 | 5.708296 | 0.0000000 | 0.0000002 |
| k__bacteria.p__firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae.g__.eubacterium. | 0.3803923 | 0.0787618 | 0.2260221 | 0.5347626 | 4.829656 | 0.0000014 | 0.0000255 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__ | 0.3369517 | 0.0781848 | 0.1837122 | 0.4901911 | 4.309681 | 0.0000163 | 0.0002707 |
| k__bacteria.p__proteobacteria.c__gammaproteobacteria.o__pasteurellales.f__pasteurellaceae.g__haemophilus | -0.2280437 | 0.0652393 | -0.3559103 | -0.1001770 | -3.495496 | 0.0004732 | 0.0064094 |
| k__bacteria.p__firmicutes.c__bacilli.o__bacillales.f__staphylococcaceae.g__staphylococcus | -0.1829793 | 0.0594315 | -0.2994629 | -0.0664956 | -3.078824 | 0.0020782 | 0.0196292 |
| k__bacteria.p__verrucomicrobia.c__verrucomicrobiae.o__verrucomicrobiales.f__verrucomicrobiaceae.g__akkermansia | 0.1907668 | 0.0798897 | 0.0341859 | 0.3473478 | 2.387877 | 0.0169460 | 0.1166765 |
| k__bacteria.p__firmicutes.c__clostridia.o__clostridiales.f__peptostreptococcaceae.g__ | 0.2910458 | 0.1410017 | 0.0146875 | 0.5674042 | 2.064129 | 0.0390054 | 0.1823383 |
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Environmental.Information.Processing..Signaling.Molecules.and.Interaction | -0.0481241 | 0.0174642 | -0.0823533 | -0.0138949 | -2.755588 | 0.0058587 | 0.2167706 |
| Genetic.Information.Processing..Transcription | 0.0159785 | 0.0066440 | 0.0029565 | 0.0290005 | 2.404959 | 0.0161743 | 0.2992240 |
Nice plot
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Metabolism..Carbohydrate.Metabolism..Fructose.and.mannose.metabolism | 0.0748047 | 0.0153469 | 0.0447254 | 0.1048841 | 4.874259 | 0.0000011 | 0.0002436 |
| Cellular.Processes..Transport.and.Catabolism..Peroxisome | -0.0634911 | 0.0150010 | -0.0928925 | -0.0340896 | -4.232451 | 0.0000231 | 0.0025774 |
| Metabolism..Lipid.Metabolism..Fatty.acid.metabolism | -0.0862183 | 0.0256901 | -0.1365700 | -0.0358667 | -3.356095 | 0.0007905 | 0.0587615 |
| Genetic.Information.Processing..Replication.and.Repair..Base.excision.repair | 0.0170264 | 0.0054765 | 0.0062925 | 0.0277602 | 3.108958 | 0.0018775 | 0.0863346 |
| Metabolism..Carbohydrate.Metabolism..Pentose.and.glucuronate.interconversions | 0.0618250 | 0.0201180 | 0.0223944 | 0.1012557 | 3.073116 | 0.0021184 | 0.0863346 |
| Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Biosynthesis.of.ansamycins | 0.0758176 | 0.0248949 | 0.0270245 | 0.1246108 | 3.045504 | 0.0023229 | 0.0863346 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Vitamin.B6.metabolism | -0.0286169 | 0.0096273 | -0.0474861 | -0.0097477 | -2.972464 | 0.0029542 | 0.0941123 |
| Metabolism..Lipid.Metabolism..Fatty.acid.biosynthesis | 0.0415976 | 0.0143916 | 0.0133905 | 0.0698047 | 2.890399 | 0.0038475 | 0.0991170 |
| Genetic.Information.Processing..Translation..Ribosome.biogenesis.in.eukaryotes | -0.0707846 | 0.0245939 | -0.1189877 | -0.0225816 | -2.878143 | 0.0040002 | 0.0991170 |
| Metabolism..Carbohydrate.Metabolism..Pentose.phosphate.pathway | 0.0339486 | 0.0122911 | 0.0098585 | 0.0580387 | 2.762045 | 0.0057441 | 0.1280925 |
| Metabolism..Metabolism.of.Other.Amino.Acids..D.Alanine.metabolism | 0.0230465 | 0.0101136 | 0.0032242 | 0.0428689 | 2.278763 | 0.0226811 | 0.4598087 |
| Unclassified..Genetic.Information.Processing..Protein.folding.and.associated.processing | -0.0110941 | 0.0050162 | -0.0209256 | -0.0012625 | -2.211653 | 0.0269906 | 0.5010248 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Drug.metabolism…other.enzymes | 0.0306056 | 0.0142804 | 0.0026166 | 0.0585946 | 2.143191 | 0.0320978 | 0.5010248 |
| Organismal.Systems..Endocrine.System..Adipocytokine.signaling.pathway | -0.1040949 | 0.0493909 | -0.2008994 | -0.0072905 | -2.107573 | 0.0350680 | 0.5010248 |
| Metabolism..Energy.Metabolism..Carbon.fixation.in.photosynthetic.organisms | 0.0263807 | 0.0125598 | 0.0017639 | 0.0509975 | 2.100403 | 0.0356934 | 0.5010248 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Drug.metabolism…cytochrome.P450 | -0.0998941 | 0.0476250 | -0.1932373 | -0.0065509 | -2.097515 | 0.0359480 | 0.5010248 |
| Human.Diseases..Infectious.Diseases..Epithelial.cell.signaling.in.Helicobacter.pylori.infection | 0.0476778 | 0.0233794 | 0.0018550 | 0.0935006 | 2.039309 | 0.0414192 | 0.5306485 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Nicotinate.and.nicotinamide.metabolism | -0.0310355 | 0.0154611 | -0.0613386 | -0.0007324 | -2.007333 | 0.0447142 | 0.5306485 |
| Metabolism..Carbohydrate.Metabolism..Amino.sugar.and.nucleotide.sugar.metabolism | 0.0289152 | 0.0146735 | 0.0001557 | 0.0576747 | 1.970575 | 0.0487726 | 0.5306485 |
Nice plot all pathways
Nice plot significant pathways only (pooled p<0.05)
Nice plot multiple testing adjusted significant pathways only (adjusted pooled p<0.1)
Level 2
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Organismal.Systems..Environmental.Adaptation | 0.0489196 | 0.0154245 | 0.0186881 | 0.0791511 | 3.171549 | 0.0015163 | 0.0561025 |
| Environmental.Information.Processing..Signaling.Molecules.and.Interaction | -0.0502036 | 0.0176101 | -0.0847186 | -0.0156885 | -2.850847 | 0.0043603 | 0.0806654 |
| Genetic.Information.Processing..Transcription | 0.0163666 | 0.0063851 | 0.0038521 | 0.0288811 | 2.563255 | 0.0103696 | 0.1278916 |
| Metabolism..Carbohydrate.Metabolism | 0.0131067 | 0.0066302 | 0.0001118 | 0.0261016 | 1.976820 | 0.0480620 | 0.4445737 |
Level 3
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Metabolism..Carbohydrate.Metabolism..Fructose.and.mannose.metabolism | 0.0806811 | 0.0162836 | 0.0487659 | 0.1125964 | 4.954756 | 0.0000007 | 0.0001622 |
| Cellular.Processes..Transport.and.Catabolism..Peroxisome | -0.0650783 | 0.0150202 | -0.0945174 | -0.0356393 | -4.332715 | 0.0000147 | 0.0016496 |
| Metabolism..Lipid.Metabolism..Fatty.acid.metabolism | -0.0946530 | 0.0230876 | -0.1399040 | -0.0494021 | -4.099727 | 0.0000414 | 0.0030885 |
| Metabolism..Carbohydrate.Metabolism..Pentose.and.glucuronate.interconversions | 0.0660993 | 0.0182315 | 0.0303662 | 0.1018323 | 3.625554 | 0.0002883 | 0.0161472 |
| Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Biosynthesis.of.ansamycins | 0.0880979 | 0.0249367 | 0.0392229 | 0.1369729 | 3.532866 | 0.0004111 | 0.0184164 |
| Metabolism..Carbohydrate.Metabolism..Pentose.phosphate.pathway | 0.0397027 | 0.0119850 | 0.0162125 | 0.0631929 | 3.312691 | 0.0009240 | 0.0301535 |
| Organismal.Systems..Environmental.Adaptation..Plant.pathogen.interaction | 0.0459717 | 0.0139004 | 0.0187273 | 0.0732161 | 3.307211 | 0.0009423 | 0.0301535 |
| Metabolism..Lipid.Metabolism..Fatty.acid.biosynthesis | 0.0443805 | 0.0142821 | 0.0163880 | 0.0723729 | 3.107413 | 0.0018873 | 0.0528452 |
| Organismal.Systems..Endocrine.System..Adipocytokine.signaling.pathway | -0.1279232 | 0.0422790 | -0.2107885 | -0.0450579 | -3.025693 | 0.0024806 | 0.0617403 |
| Genetic.Information.Processing..Translation..Ribosome.biogenesis.in.eukaryotes | -0.0721010 | 0.0246330 | -0.1203808 | -0.0238213 | -2.927011 | 0.0034224 | 0.0766609 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Vitamin.B6.metabolism | -0.0291619 | 0.0100993 | -0.0489563 | -0.0093676 | -2.887504 | 0.0038831 | 0.0790743 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Porphyrin.and.chlorophyll.metabolism | 0.0626417 | 0.0223883 | 0.0187615 | 0.1065219 | 2.797970 | 0.0051425 | 0.0959931 |
| Metabolism..Energy.Metabolism..Carbon.fixation.in.photosynthetic.organisms | 0.0364030 | 0.0131564 | 0.0106170 | 0.0621889 | 2.766949 | 0.0056584 | 0.0974979 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Drug.metabolism…other.enzymes | 0.0353067 | 0.0131936 | 0.0094477 | 0.0611657 | 2.676042 | 0.0074497 | 0.1191955 |
| Genetic.Information.Processing..Replication.and.Repair..Base.excision.repair | 0.0148692 | 0.0057662 | 0.0035677 | 0.0261706 | 2.578692 | 0.0099175 | 0.1481015 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Biotin.metabolism | 0.0443338 | 0.0180359 | 0.0089842 | 0.0796835 | 2.458094 | 0.0139677 | 0.1955472 |
| Unclassified..Cellular.Processes.and.Signaling..Inorganic.ion.transport.and.metabolism | -0.0854735 | 0.0363810 | -0.1567790 | -0.0141680 | -2.349397 | 0.0188039 | 0.2441364 |
| Metabolism..Lipid.Metabolism..Glycerolipid.metabolism | 0.0381790 | 0.0163608 | 0.0061125 | 0.0702456 | 2.333573 | 0.0196181 | 0.2441364 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Toluene.degradation | -0.0789239 | 0.0346447 | -0.1468262 | -0.0110215 | -2.278094 | 0.0227210 | 0.2625265 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Drug.metabolism…cytochrome.P450 | -0.1077738 | 0.0475573 | -0.2009843 | -0.0145632 | -2.266188 | 0.0234399 | 0.2625265 |
| Organismal.Systems..Endocrine.System..Insulin.signaling.pathway | 0.0604418 | 0.0275299 | 0.0064843 | 0.1143993 | 2.195500 | 0.0281278 | 0.2934589 |
| Unclassified..Genetic.Information.Processing..Protein.folding.and.associated.processing | -0.0110271 | 0.0050446 | -0.0209143 | -0.0011398 | -2.185914 | 0.0288219 | 0.2934589 |
| Metabolism..Metabolism.of.Other.Amino.Acids..D.Alanine.metabolism | 0.0214157 | 0.0100361 | 0.0017453 | 0.0410862 | 2.133866 | 0.0328537 | 0.3199669 |
| Metabolism..Amino.Acid.Metabolism..Glycine..serine.and.threonine.metabolism | -0.0151926 | 0.0072327 | -0.0293685 | -0.0010168 | -2.100542 | 0.0356812 | 0.3248701 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Nicotinate.and.nicotinamide.metabolism | -0.0326563 | 0.0156489 | -0.0633275 | -0.0019850 | -2.086812 | 0.0369051 | 0.3248701 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Metabolism.of.xenobiotics.by.cytochrome.P450 | -0.0993704 | 0.0480715 | -0.1935887 | -0.0051520 | -2.067137 | 0.0387213 | 0.3248701 |
| Genetic.Information.Processing..Translation..RNA.transport | 0.0621342 | 0.0301254 | 0.0030895 | 0.1211788 | 2.062518 | 0.0391584 | 0.3248701 |
| Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Tetracycline.biosynthesis | 0.0562197 | 0.0281702 | 0.0010072 | 0.1114323 | 1.995717 | 0.0459647 | 0.3514947 |
| Genetic.Information.Processing..Folding..Sorting.and.Degradation..Proteasome | -0.0963819 | 0.0484326 | -0.1913081 | -0.0014557 | -1.990020 | 0.0465887 | 0.3514947 |
| Human.Diseases..Infectious.Diseases..Epithelial.cell.signaling.in.Helicobacter.pylori.infection | 0.0458477 | 0.0231344 | 0.0005050 | 0.0911903 | 1.981795 | 0.0475022 | 0.3514947 |
| Metabolism..Carbohydrate.Metabolism..Amino.sugar.and.nucleotide.sugar.metabolism | 0.0282869 | 0.0143465 | 0.0001683 | 0.0564055 | 1.971696 | 0.0486444 | 0.3514947 |
Level 2
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Metabolism..Glycan.Biosynthesis.and.Metabolism | 0.0519612 | 0.0115735 | 0.0292776 | 0.0746448 | 4.489673 | 0.0000071 | 0.0002639 |
| Genetic.Information.Processing..Transcription | 0.0140217 | 0.0051204 | 0.0039858 | 0.0240575 | 2.738388 | 0.0061741 | 0.1142213 |
| Environmental.Information.Processing..Signaling.Molecules.and.Interaction | -0.0463997 | 0.0186814 | -0.0830146 | -0.0097848 | -2.483737 | 0.0130012 | 0.1603479 |
Level 3
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Metabolism..Carbohydrate.Metabolism..Fructose.and.mannose.metabolism | 0.0695846 | 0.0140831 | 0.0419821 | 0.0971870 | 4.940987 | 0.0000008 | 0.0001757 |
| Cellular.Processes..Transport.and.Catabolism..Peroxisome | -0.0593738 | 0.0158836 | -0.0905051 | -0.0282425 | -3.738054 | 0.0001854 | 0.0209558 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Xylene.degradation | -0.0564881 | 0.0187429 | -0.0932235 | -0.0197527 | -3.013838 | 0.0025797 | 0.1577341 |
| Metabolism..Lipid.Metabolism..Fatty.acid.metabolism | -0.0893386 | 0.0299073 | -0.1479559 | -0.0307213 | -2.987181 | 0.0028156 | 0.1577341 |
| Genetic.Information.Processing..Folding..Sorting.and.Degradation..Chaperones.and.folding.catalysts | 0.0242035 | 0.0083216 | 0.0078934 | 0.0405136 | 2.908510 | 0.0036316 | 0.1577341 |
| Genetic.Information.Processing..Translation..Ribosome.biogenesis.in.eukaryotes | -0.0711084 | 0.0249038 | -0.1199190 | -0.0222978 | -2.855322 | 0.0042993 | 0.1577341 |
| Metabolism..Carbohydrate.Metabolism..Pentose.and.glucuronate.interconversions | 0.0503206 | 0.0179765 | 0.0150873 | 0.0855539 | 2.799240 | 0.0051223 | 0.1577341 |
| Metabolism..Lipid.Metabolism..Fatty.acid.biosynthesis | 0.0451811 | 0.0163033 | 0.0132272 | 0.0771349 | 2.771288 | 0.0055835 | 0.1577341 |
| Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Biosynthesis.of.ansamycins | 0.0717378 | 0.0274480 | 0.0179408 | 0.1255348 | 2.613593 | 0.0089596 | 0.2249850 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Vitamin.B6.metabolism | -0.0243667 | 0.0095096 | -0.0430052 | -0.0057281 | -2.562315 | 0.0103977 | 0.2302045 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Biotin.metabolism | 0.0480086 | 0.0190681 | 0.0106359 | 0.0853814 | 2.517749 | 0.0118107 | 0.2302045 |
| Metabolism..Carbohydrate.Metabolism..Pentose.phosphate.pathway | 0.0334309 | 0.0133423 | 0.0072805 | 0.0595814 | 2.505633 | 0.0122232 | 0.2302045 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Drug.metabolism…other.enzymes | 0.0381120 | 0.0159839 | 0.0067842 | 0.0694399 | 2.384403 | 0.0171069 | 0.2973962 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Chloroalkane.and.chloroalkene.degradation | -0.0440491 | 0.0187390 | -0.0807769 | -0.0073214 | -2.350670 | 0.0187396 | 0.3025111 |
| Genetic.Information.Processing..Replication.and.Repair..Base.excision.repair | 0.0136657 | 0.0059388 | 0.0020258 | 0.0253056 | 2.301070 | 0.0213877 | 0.3222407 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Drug.metabolism…cytochrome.P450 | -0.1047320 | 0.0486254 | -0.2000359 | -0.0094280 | -2.153855 | 0.0312515 | 0.4116602 |
| Environmental.Information.Processing..Signal.Transduction..Phosphatidylinositol.signaling.system | 0.0181668 | 0.0084431 | 0.0016186 | 0.0347150 | 2.151673 | 0.0314231 | 0.4116602 |
| Metabolism..Energy.Metabolism..Carbon.fixation.in.photosynthetic.organisms | 0.0344968 | 0.0161602 | 0.0028235 | 0.0661702 | 2.134681 | 0.0327871 | 0.4116602 |
| Metabolism..Metabolism.of.Other.Amino.Acids..D.Alanine.metabolism | 0.0224208 | 0.0107122 | 0.0014253 | 0.0434164 | 2.093014 | 0.0363479 | 0.4323489 |
| Genetic.Information.Processing..Folding..Sorting.and.Degradation..Proteasome | -0.1014237 | 0.0500534 | -0.1995265 | -0.0033209 | -2.026311 | 0.0427329 | 0.4828817 |
Level 2
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Environmental.Information.Processing..Signaling.Molecules.and.Interaction | -0.0481241 | 0.0174642 | -0.0823533 | -0.0138949 | -2.755588 | 0.0058587 | 0.2167706 |
| Genetic.Information.Processing..Transcription | 0.0159785 | 0.0066440 | 0.0029565 | 0.0290005 | 2.404959 | 0.0161743 | 0.2992240 |
Level 3
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Metabolism..Carbohydrate.Metabolism..Fructose.and.mannose.metabolism | 0.0748047 | 0.0153469 | 0.0447254 | 0.1048841 | 4.874259 | 0.0000011 | 0.0002468 |
| Cellular.Processes..Transport.and.Catabolism..Peroxisome | -0.0634911 | 0.0150010 | -0.0928925 | -0.0340896 | -4.232451 | 0.0000231 | 0.0026121 |
| Metabolism..Lipid.Metabolism..Fatty.acid.metabolism | -0.0862183 | 0.0256901 | -0.1365700 | -0.0358667 | -3.356095 | 0.0007905 | 0.0595520 |
| Genetic.Information.Processing..Replication.and.Repair..Base.excision.repair | 0.0170264 | 0.0054765 | 0.0062925 | 0.0277602 | 3.108958 | 0.0018775 | 0.0874960 |
| Metabolism..Carbohydrate.Metabolism..Pentose.and.glucuronate.interconversions | 0.0618250 | 0.0201180 | 0.0223944 | 0.1012557 | 3.073116 | 0.0021184 | 0.0874960 |
| Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Biosynthesis.of.ansamycins | 0.0758176 | 0.0248949 | 0.0270245 | 0.1246108 | 3.045504 | 0.0023229 | 0.0874960 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Vitamin.B6.metabolism | -0.0286169 | 0.0096273 | -0.0474861 | -0.0097477 | -2.972464 | 0.0029542 | 0.0953784 |
| Metabolism..Lipid.Metabolism..Fatty.acid.biosynthesis | 0.0415976 | 0.0143916 | 0.0133905 | 0.0698047 | 2.890399 | 0.0038475 | 0.1004504 |
| Genetic.Information.Processing..Translation..Ribosome.biogenesis.in.eukaryotes | -0.0707846 | 0.0245939 | -0.1189877 | -0.0225816 | -2.878143 | 0.0040002 | 0.1004504 |
| Metabolism..Carbohydrate.Metabolism..Pentose.phosphate.pathway | 0.0339486 | 0.0122911 | 0.0098585 | 0.0580387 | 2.762045 | 0.0057441 | 0.1298157 |
| Metabolism..Metabolism.of.Other.Amino.Acids..D.Alanine.metabolism | 0.0230465 | 0.0101136 | 0.0032242 | 0.0428689 | 2.278763 | 0.0226811 | 0.4659945 |
| Unclassified..Genetic.Information.Processing..Protein.folding.and.associated.processing | -0.0110941 | 0.0050162 | -0.0209256 | -0.0012625 | -2.211653 | 0.0269906 | 0.5077651 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Drug.metabolism…other.enzymes | 0.0306056 | 0.0142804 | 0.0026166 | 0.0585946 | 2.143191 | 0.0320978 | 0.5077651 |
| Organismal.Systems..Endocrine.System..Adipocytokine.signaling.pathway | -0.1040949 | 0.0493909 | -0.2008994 | -0.0072905 | -2.107573 | 0.0350680 | 0.5077651 |
| Metabolism..Energy.Metabolism..Carbon.fixation.in.photosynthetic.organisms | 0.0263807 | 0.0125598 | 0.0017639 | 0.0509975 | 2.100403 | 0.0356934 | 0.5077651 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Drug.metabolism…cytochrome.P450 | -0.0998941 | 0.0476250 | -0.1932373 | -0.0065509 | -2.097515 | 0.0359480 | 0.5077651 |
| Human.Diseases..Infectious.Diseases..Epithelial.cell.signaling.in.Helicobacter.pylori.infection | 0.0476778 | 0.0233794 | 0.0018550 | 0.0935006 | 2.039309 | 0.0414192 | 0.5377872 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Nicotinate.and.nicotinamide.metabolism | -0.0310355 | 0.0154611 | -0.0613386 | -0.0007324 | -2.007333 | 0.0447142 | 0.5377872 |
| Metabolism..Carbohydrate.Metabolism..Amino.sugar.and.nucleotide.sugar.metabolism | 0.0289152 | 0.0146735 | 0.0001557 | 0.0576747 | 1.970575 | 0.0487726 | 0.5377872 |
Level 2
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Human.Diseases..Infectious.Diseases | -0.0484981 | 0.0139289 | -0.0757982 | -0.0211980 | -3.481839 | 0.0004980 | 0.0189234 |
| Human.Diseases..Neurodegenerative.Diseases | -0.0840083 | 0.0286090 | -0.1400809 | -0.0279357 | -2.936430 | 0.0033201 | 0.0630826 |
| Unclassified..Genetic.Information.Processing | -0.0202899 | 0.0083563 | -0.0366680 | -0.0039118 | -2.428091 | 0.0151785 | 0.1607306 |
| Environmental.Information.Processing..Signal.Transduction | -0.0553524 | 0.0231749 | -0.1007744 | -0.0099304 | -2.388463 | 0.0169190 | 0.1607306 |
| Metabolism..Metabolism.of.Other.Amino.Acids | -0.0167393 | 0.0076171 | -0.0316685 | -0.0018101 | -2.197602 | 0.0279775 | 0.2126291 |
Level 3 All
Significant only (pooled p<0.05)
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Metabolism..Carbohydrate.Metabolism..Pentose.phosphate.pathway | 0.0461974 | 0.0092376 | 0.0280921 | 0.0643027 | 5.001030 | 0.0000006 | 0.0001306 |
| Metabolism..Carbohydrate.Metabolism..Propanoate.metabolism | -0.0570404 | 0.0134718 | -0.0834447 | -0.0306362 | -4.234055 | 0.0000230 | 0.0026279 |
| Metabolism..Lipid.Metabolism..Fatty.acid.metabolism | -0.0993213 | 0.0284718 | -0.1551250 | -0.0435176 | -3.488412 | 0.0004859 | 0.0370903 |
| Metabolism..Carbohydrate.Metabolism..Fructose.and.mannose.metabolism | 0.0720518 | 0.0219622 | 0.0290068 | 0.1150969 | 3.280725 | 0.0010354 | 0.0592770 |
| Unclassified..Cellular.Processes.and.Signaling..Sporulation | 0.2691131 | 0.0880246 | 0.0965881 | 0.4416381 | 3.057250 | 0.0022338 | 0.0994375 |
| Metabolism..Carbohydrate.Metabolism..Amino.sugar.and.nucleotide.sugar.metabolism | 0.0398818 | 0.0132461 | 0.0139199 | 0.0658437 | 3.010830 | 0.0026054 | 0.0994375 |
| Metabolism..Enzyme.Families..Peptidases | 0.0213727 | 0.0072551 | 0.0071530 | 0.0355924 | 2.945901 | 0.0032202 | 0.1053451 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Pantothenate.and.CoA.biosynthesis | 0.0229267 | 0.0086275 | 0.0060172 | 0.0398362 | 2.657414 | 0.0078743 | 0.2154792 |
| Metabolism..Energy.Metabolism..Carbon.fixation.in.photosynthetic.organisms | 0.0343939 | 0.0132238 | 0.0084757 | 0.0603121 | 2.600904 | 0.0092979 | 0.2154792 |
| Metabolism..Carbohydrate.Metabolism..Butanoate.metabolism | -0.0390622 | 0.0152890 | -0.0690281 | -0.0090962 | -2.554916 | 0.0106214 | 0.2154792 |
| Metabolism..Metabolism.of.Other.Amino.Acids..Glutathione.metabolism | -0.0759232 | 0.0298932 | -0.1345127 | -0.0173336 | -2.539817 | 0.0110911 | 0.2154792 |
| Metabolism..Amino.Acid.Metabolism..Tryptophan.metabolism | -0.1037075 | 0.0410760 | -0.1842150 | -0.0232001 | -2.524773 | 0.0115773 | 0.2154792 |
| Metabolism..Amino.Acid.Metabolism..Lysine.degradation | -0.0938693 | 0.0377849 | -0.1679263 | -0.0198124 | -2.484310 | 0.0129803 | 0.2154792 |
| Environmental.Information.Processing..Membrane.Transport..Bacterial.secretion.system | -0.0478536 | 0.0193032 | -0.0856872 | -0.0100200 | -2.479047 | 0.0131734 | 0.2154792 |
| Unclassified..Genetic.Information.Processing..Replication..recombination.and.repair.proteins | -0.0443230 | 0.0181120 | -0.0798220 | -0.0088241 | -2.447159 | 0.0143987 | 0.2198206 |
| Environmental.Information.Processing..Signal.Transduction..Two.component.system | -0.0610081 | 0.0262962 | -0.1125477 | -0.0094685 | -2.320034 | 0.0203390 | 0.2911026 |
| Metabolism..Carbohydrate.Metabolism..Pentose.and.glucuronate.interconversions | 0.0597831 | 0.0266534 | 0.0075434 | 0.1120228 | 2.242983 | 0.0248979 | 0.3300089 |
| Metabolism..Lipid.Metabolism..Sphingolipid.metabolism | 0.0973295 | 0.0437020 | 0.0116751 | 0.1829839 | 2.227115 | 0.0259396 | 0.3300089 |
| Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Limonene.and.pinene.degradation | -0.0813978 | 0.0386717 | -0.1571928 | -0.0056027 | -2.104844 | 0.0353049 | 0.4255172 |
| Metabolism..Amino.Acid.Metabolism..Valine..leucine.and.isoleucine.degradation | -0.0895058 | 0.0434446 | -0.1746557 | -0.0043559 | -2.060227 | 0.0393768 | 0.4326503 |
| Metabolism..Energy.Metabolism..Methane.metabolism | 0.0355941 | 0.0173608 | 0.0015675 | 0.0696207 | 2.050251 | 0.0403400 | 0.4326503 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Vitamin.B6.metabolism | -0.0328569 | 0.0162180 | -0.0646435 | -0.0010703 | -2.025958 | 0.0427691 | 0.4326503 |
| Organismal.Systems..Endocrine.System..Insulin.signaling.pathway | 0.0703689 | 0.0351516 | 0.0014731 | 0.1392648 | 2.001871 | 0.0452986 | 0.4326503 |
| Environmental.Information.Processing..Membrane.Transport..Secretion.system | -0.0508999 | 0.0255435 | -0.1009642 | -0.0008357 | -1.992679 | 0.0462966 | 0.4326503 |
| Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Biosynthesis.of.ansamycins | 0.0805279 | 0.0405844 | 0.0009840 | 0.1600719 | 1.984209 | 0.0472326 | 0.4326503 |
Multiple testing adjusted Significant only (adjusted pooled p<0.1)
Level 2
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Human.Diseases..Infectious.Diseases | -0.1126764 | 0.0258973 | -0.1634341 | -0.0619188 | -4.350903 | 0.0000136 | 0.0005152 |
| Environmental.Information.Processing..Signal.Transduction | -0.1416460 | 0.0372818 | -0.2147171 | -0.0685750 | -3.799334 | 0.0001451 | 0.0027566 |
| Unclassified..Poorly.Characterized | -0.1803121 | 0.0692044 | -0.3159502 | -0.0446739 | -2.605500 | 0.0091740 | 0.0868309 |
| Metabolism..Energy.Metabolism | 0.0374528 | 0.0147283 | 0.0085859 | 0.0663197 | 2.542920 | 0.0109930 | 0.0868309 |
| Human.Diseases..Neurodegenerative.Diseases | -0.1436055 | 0.0567741 | -0.2548806 | -0.0323303 | -2.529420 | 0.0114251 | 0.0868309 |
| Genetic.Information.Processing..Replication.and.Repair | 0.1053877 | 0.0472699 | 0.0127404 | 0.1980350 | 2.229488 | 0.0257815 | 0.1311394 |
| Metabolism..Nucleotide.Metabolism | 0.1138804 | 0.0510945 | 0.0137370 | 0.2140238 | 2.228820 | 0.0258259 | 0.1311394 |
| Metabolism..Amino.Acid.Metabolism | 0.0256341 | 0.0117885 | 0.0025291 | 0.0487391 | 2.174502 | 0.0296674 | 0.1311394 |
| Unclassified..Cellular.Processes.and.Signaling | -0.1513433 | 0.0711795 | -0.2908525 | -0.0118341 | -2.126222 | 0.0334848 | 0.1311394 |
| Metabolism..Carbohydrate.Metabolism | 0.0257629 | 0.0121865 | 0.0018779 | 0.0496480 | 2.114057 | 0.0345104 | 0.1311394 |
Level 3 All
Significant only (pooled p<0.05)
| estimate.nebf | se.nebf | ll.nebf | ul.nebf | z.nebf | p.nebf | p.adjust.nebf | |
|---|---|---|---|---|---|---|---|
| Metabolism..Amino.Acid.Metabolism..Lysine.degradation | -0.2410428 | 0.0589751 | -0.3566318 | -0.1254538 | -4.087199 | 0.0000437 | 0.0052013 |
| Environmental.Information.Processing..Membrane.Transport..Secretion.system | -0.1668053 | 0.0409038 | -0.2469752 | -0.0866354 | -4.077994 | 0.0000454 | 0.0052013 |
| Cellular.Processes..Cell.Motility..Cytoskeleton.proteins | 0.1946407 | 0.0501812 | 0.0962873 | 0.2929941 | 3.878754 | 0.0001050 | 0.0080144 |
| Environmental.Information.Processing..Signal.Transduction..Two.component.system | -0.1563058 | 0.0417345 | -0.2381040 | -0.0745076 | -3.745237 | 0.0001802 | 0.0103178 |
| Metabolism..Amino.Acid.Metabolism..Lysine.biosynthesis | 0.0932496 | 0.0261242 | 0.0420471 | 0.1444521 | 3.569470 | 0.0003577 | 0.0147737 |
| Metabolism..Amino.Acid.Metabolism..Tryptophan.metabolism | -0.2173867 | 0.0612575 | -0.3374491 | -0.0973242 | -3.548736 | 0.0003871 | 0.0147737 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Thiamine.metabolism | 0.0778945 | 0.0227453 | 0.0333146 | 0.1224745 | 3.424647 | 0.0006156 | 0.0201389 |
| Metabolism..Lipid.Metabolism..Biosynthesis.of.unsaturated.fatty.acids | -0.1598449 | 0.0480023 | -0.2539276 | -0.0657621 | -3.329941 | 0.0008686 | 0.0248649 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Drug.metabolism…other.enzymes | 0.0699567 | 0.0212525 | 0.0283025 | 0.1116109 | 3.291685 | 0.0009959 | 0.0253399 |
| Metabolism..Lipid.Metabolism..Fatty.acid.metabolism | -0.1490154 | 0.0458870 | -0.2389524 | -0.0590784 | -3.247440 | 0.0011645 | 0.0266667 |
| Genetic.Information.Processing..Folding..Sorting.and.Degradation..Sulfur.relay.system | -0.1371891 | 0.0433387 | -0.2221315 | -0.0522467 | -3.165507 | 0.0015481 | 0.0299670 |
| Metabolism..Carbohydrate.Metabolism..Galactose.metabolism | 0.1151450 | 0.0364226 | 0.0437581 | 0.1865320 | 3.161364 | 0.0015703 | 0.0299670 |
| Genetic.Information.Processing..Replication.and.Repair..Mismatch.repair | 0.0832394 | 0.0269024 | 0.0305117 | 0.1359671 | 3.094126 | 0.0019739 | 0.0347716 |
| Metabolism..Enzyme.Families..Peptidases | 0.0367908 | 0.0120243 | 0.0132236 | 0.0603581 | 3.059696 | 0.0022156 | 0.0362412 |
| Unclassified..Cellular.Processes.and.Signaling..Inorganic.ion.transport.and.metabolism | -0.2280142 | 0.0753721 | -0.3757408 | -0.0802875 | -3.025179 | 0.0024849 | 0.0378887 |
| Metabolism..Biosynthesis.of.Other.Secondary.Metabolites..Phenylpropanoid.biosynthesis | 0.1624628 | 0.0543283 | 0.0559814 | 0.2689443 | 2.990393 | 0.0027862 | 0.0378887 |
| Genetic.Information.Processing..Replication.and.Repair..Nucleotide.excision.repair | 0.1893190 | 0.0633790 | 0.0650986 | 0.3135395 | 2.987096 | 0.0028164 | 0.0378887 |
| Metabolism..Carbohydrate.Metabolism..Amino.sugar.and.nucleotide.sugar.metabolism | 0.0854708 | 0.0289330 | 0.0287632 | 0.1421784 | 2.954096 | 0.0031359 | 0.0378887 |
| Genetic.Information.Processing..Replication.and.Repair..DNA.replication.proteins | 0.0714555 | 0.0241948 | 0.0240344 | 0.1188765 | 2.953335 | 0.0031436 | 0.0378887 |
| Unclassified..Cellular.Processes.and.Signaling..Sporulation | 0.4258710 | 0.1509691 | 0.1299770 | 0.7217649 | 2.820915 | 0.0047887 | 0.0548305 |
| Unclassified..Cellular.Processes.and.Signaling..Other.ion.coupled.transporters | -0.1077009 | 0.0387677 | -0.1836842 | -0.0317177 | -2.778113 | 0.0054676 | 0.0596224 |
| Metabolism..Amino.Acid.Metabolism..Valine..leucine.and.isoleucine.degradation | -0.1456712 | 0.0536771 | -0.2508764 | -0.0404661 | -2.713844 | 0.0066508 | 0.0666673 |
| Metabolism..Metabolism.of.Other.Amino.Acids..Glutathione.metabolism | -0.1200119 | 0.0442873 | -0.2068134 | -0.0332105 | -2.709852 | 0.0067313 | 0.0666673 |
| Metabolism..Energy.Metabolism..Carbon.fixation.in.photosynthetic.organisms | 0.0526806 | 0.0195297 | 0.0144032 | 0.0909581 | 2.697465 | 0.0069870 | 0.0666673 |
| Unclassified..Metabolism..Metabolism.of.cofactors.and.vitamins | -0.1333637 | 0.0498366 | -0.2310416 | -0.0356858 | -2.676021 | 0.0074502 | 0.0682438 |
| Human.Diseases..Infectious.Diseases..Vibrio.cholerae.pathogenic.cycle | -0.1267418 | 0.0476819 | -0.2201966 | -0.0332870 | -2.658069 | 0.0078590 | 0.0692195 |
| Metabolism..Nucleotide.Metabolism..Pyrimidine.metabolism | 0.1104510 | 0.0429456 | 0.0262793 | 0.1946228 | 2.571884 | 0.0101147 | 0.0815516 |
| Metabolism..Amino.Acid.Metabolism..Phenylalanine..tyrosine.and.tryptophan.biosynthesis | 0.0758791 | 0.0298059 | 0.0174605 | 0.1342977 | 2.545772 | 0.0109036 | 0.0815516 |
| Unclassified..Poorly.Characterized..Function.unknown | -0.1569012 | 0.0616904 | -0.2778123 | -0.0359902 | -2.543364 | 0.0109791 | 0.0815516 |
| Unclassified..Metabolism..Biosynthesis.and.biodegradation.of.secondary.metabolites | -0.2158734 | 0.0850259 | -0.3825210 | -0.0492257 | -2.538914 | 0.0111197 | 0.0815516 |
| Metabolism..Enzyme.Families..Protein.kinases | -0.1293255 | 0.0510231 | -0.2293288 | -0.0293222 | -2.534648 | 0.0112560 | 0.0815516 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..One.carbon.pool.by.folate | 0.1439633 | 0.0568953 | 0.0324506 | 0.2554761 | 2.530320 | 0.0113959 | 0.0815516 |
| Metabolism..Energy.Metabolism..Methane.metabolism | 0.0633891 | 0.0251859 | 0.0140256 | 0.1127526 | 2.516847 | 0.0118410 | 0.0821696 |
| Cellular.Processes..Cell.Growth.and.Death..Cell.cycle…Caulobacter | 0.2069000 | 0.0840125 | 0.0422384 | 0.3715616 | 2.462727 | 0.0137885 | 0.0928694 |
| Genetic.Information.Processing..Replication.and.Repair..DNA.replication | 0.0956593 | 0.0391391 | 0.0189480 | 0.1723706 | 2.444083 | 0.0145221 | 0.0950160 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Ubiquinone.and.other.terpenoid.quinone.biosynthesis | -0.1294977 | 0.0541391 | -0.2356083 | -0.0233871 | -2.391946 | 0.0167593 | 0.1066077 |
| Human.Diseases..Infectious.Diseases..Pertussis | -0.3459067 | 0.1463292 | -0.6327068 | -0.0591067 | -2.363893 | 0.0180840 | 0.1119254 |
| Metabolism..Carbohydrate.Metabolism..Starch.and.sucrose.metabolism | 0.0968519 | 0.0416485 | 0.0152222 | 0.1784815 | 2.325456 | 0.0200476 | 0.1186550 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Polycyclic.aromatic.hydrocarbon.degradation | 0.1728426 | 0.0745087 | 0.0268082 | 0.3188769 | 2.319764 | 0.0203536 | 0.1186550 |
| Metabolism..Metabolism.of.Cofactors.and.Vitamins..Pantothenate.and.CoA.biosynthesis | 0.0398297 | 0.0172203 | 0.0060784 | 0.0735810 | 2.312943 | 0.0207258 | 0.1186550 |
| Unclassified..Cellular.Processes.and.Signaling..Electron.transfer.carriers | -0.3152297 | 0.1370671 | -0.5838763 | -0.0465831 | -2.299820 | 0.0214584 | 0.1198530 |
| Cellular.Processes..Cell.Motility..Bacterial.motility.proteins | -0.1964298 | 0.0868495 | -0.3666517 | -0.0262078 | -2.261725 | 0.0237144 | 0.1292999 |
| Metabolism..Amino.Acid.Metabolism..Amino.acid.related.enzymes | 0.1029036 | 0.0459318 | 0.0128789 | 0.1929283 | 2.240355 | 0.0250679 | 0.1335010 |
| Metabolism..Glycan.Biosynthesis.and.Metabolism..Peptidoglycan.biosynthesis | 0.1655029 | 0.0742134 | 0.0200473 | 0.3109585 | 2.230095 | 0.0257412 | 0.1337390 |
| Metabolism..Glycan.Biosynthesis.and.Metabolism..Lipopolysaccharide.biosynthesis.proteins | -0.4913860 | 0.2211418 | -0.9248161 | -0.0579560 | -2.222040 | 0.0262806 | 0.1337390 |
| Unclassified..Cellular.Processes.and.Signaling..Membrane.and.intracellular.structural.molecules | -0.3249676 | 0.1470898 | -0.6132583 | -0.0366768 | -2.209314 | 0.0271528 | 0.1338000 |
| Metabolism..Energy.Metabolism..Photosynthesis | 0.3092523 | 0.1402569 | 0.0343539 | 0.5841507 | 2.204900 | 0.0274611 | 0.1338000 |
| Metabolism..Energy.Metabolism..Photosynthesis.proteins | 0.2924081 | 0.1367362 | 0.0244100 | 0.5604062 | 2.138483 | 0.0324776 | 0.1419698 |
| Genetic.Information.Processing..Replication.and.Repair..Homologous.recombination | 0.1521295 | 0.0711988 | 0.0125825 | 0.2916766 | 2.136688 | 0.0326234 | 0.1419698 |
| Genetic.Information.Processing..Folding..Sorting.and.Degradation..Protein.export | 0.2001823 | 0.0937140 | 0.0165063 | 0.3838583 | 2.136099 | 0.0326714 | 0.1419698 |
| Metabolism..Lipid.Metabolism..Sphingolipid.metabolism | 0.3160602 | 0.1483752 | 0.0252501 | 0.6068702 | 2.130141 | 0.0331600 | 0.1419698 |
| Genetic.Information.Processing..Translation..Translation.factors | 0.1979245 | 0.0932695 | 0.0151195 | 0.3807294 | 2.122070 | 0.0338319 | 0.1419698 |
| Genetic.Information.Processing..Replication.and.Repair..DNA.repair.and.recombination.proteins | 0.1416179 | 0.0668713 | 0.0105526 | 0.2726833 | 2.117768 | 0.0341947 | 0.1419698 |
| Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Prenyltransferases | 0.0689059 | 0.0325922 | 0.0050264 | 0.1327855 | 2.114184 | 0.0344996 | 0.1419698 |
| Unclassified..Poorly.Characterized..General.function.prediction.only | -0.1479579 | 0.0699906 | -0.2851369 | -0.0107788 | -2.113968 | 0.0345180 | 0.1419698 |
| Unclassified..Cellular.Processes.and.Signaling..Signal.transduction.mechanisms | -0.1179107 | 0.0558385 | -0.2273522 | -0.0084693 | -2.111638 | 0.0347175 | 0.1419698 |
| Metabolism..Metabolism.of.Other.Amino.Acids..beta.Alanine.metabolism | -0.1460591 | 0.0714335 | -0.2860661 | -0.0060521 | -2.044687 | 0.0408857 | 0.1642602 |
| Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Limonene.and.pinene.degradation | -0.1832241 | 0.0900308 | -0.3596813 | -0.0067669 | -2.035126 | 0.0418382 | 0.1651887 |
| Metabolism..Metabolism.of.Terpenoids.and.Polyketides..Biosynthesis.of.siderophore.group.nonribosomal.peptides | -0.2787206 | 0.1381849 | -0.5495580 | -0.0078831 | -2.017012 | 0.0436943 | 0.1690090 |
| Genetic.Information.Processing..Translation..Ribosome | 0.2622067 | 0.1303595 | 0.0067069 | 0.5177065 | 2.011413 | 0.0442818 | 0.1690090 |
| Metabolism..Xenobiotics.Biodegradation.and.Metabolism..Toluene.degradation | -0.0942549 | 0.0471773 | -0.1867207 | -0.0017891 | -1.997887 | 0.0457289 | 0.1716708 |
| Genetic.Information.Processing..Replication.and.Repair..Chromosome | 0.0281142 | 0.0141358 | 0.0004085 | 0.0558200 | 1.988861 | 0.0467165 | 0.1725498 |
| Metabolism..Carbohydrate.Metabolism..Glyoxylate.and.dicarboxylate.metabolism | -0.0952237 | 0.0482937 | -0.1898776 | -0.0005698 | -1.971762 | 0.0486368 | 0.1767908 |
Multiple testing adjusted Significant only (adjusted pooled p<0.1)
All analyses are adjusted for age of infants or breastfeeding status at sample collection and accounting for repeated/longitudinal sample collection.
For Subramanian (Bangladesh) data only.
Change in taxa relative abundance in duration of exclusive bf >2months vs. <=2 months
GAMLSS
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| firmicutes | -0.2451898 | 0.0633103 | -3.872828 | 0.0001188 | 0.0004750 | -0.3692779 | -0.1211016 |
| actinobacteria | 0.2267863 | 0.0709545 | 3.196223 | 0.0014620 | 0.0029239 | 0.0877156 | 0.3658570 |
GAMLSS
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| actinobacteria.c__coriobacteriia.o__coriobacteriales | -0.2485089 | 0.0652555 | -3.808244 | 0.0001536 | 0.0007304 | -0.3764097 | -0.1206081 |
| firmicutes.c__bacilli.o__lactobacillales | -0.2705907 | 0.0725448 | -3.729979 | 0.0002087 | 0.0007304 | -0.4127786 | -0.1284028 |
| actinobacteria.c__actinobacteria.o__bifidobacteriales | 0.2543014 | 0.0712188 | 3.570704 | 0.0003831 | 0.0008938 | 0.1147125 | 0.3938904 |
| firmicutes.c__erysipelotrichi.o__erysipelotrichales | -0.1523709 | 0.0757899 | -2.010438 | 0.0448092 | 0.0784160 | -0.3009192 | -0.0038227 |
GAMLSS
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| firmicutes.c__bacilli.o__lactobacillales.f__lactobacillaceae | -0.3106381 | 0.0757692 | -4.099792 | 0.0000467 | 0.0006074 | -0.4591458 | -0.1621304 |
| actinobacteria.c__coriobacteriia.o__coriobacteriales.f__coriobacteriaceae | -0.2485089 | 0.0652555 | -3.808244 | 0.0001536 | 0.0009984 | -0.3764097 | -0.1206081 |
| actinobacteria.c__actinobacteria.o__bifidobacteriales.f__bifidobacteriaceae | 0.2543014 | 0.0712188 | 3.570704 | 0.0003831 | 0.0016600 | 0.1147125 | 0.3938904 |
| bacteroidetes.c__bacteroidia.o__bacteroidales.f__prevotellaceae | -0.2684295 | 0.0800336 | -3.353959 | 0.0008441 | 0.0027434 | -0.4252954 | -0.1115636 |
| firmicutes.c__clostridia.o__clostridiales.f__clostridiaceae | -0.2173273 | 0.0799003 | -2.719980 | 0.0067053 | 0.0174337 | -0.3739319 | -0.0607226 |
| firmicutes.c__bacilli.o__lactobacillales.f__enterococcaceae | 0.1916596 | 0.0817407 | 2.344727 | 0.0193459 | 0.0419160 | 0.0314478 | 0.3518714 |
| firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae | -0.1523709 | 0.0757899 | -2.010438 | 0.0448092 | 0.0789058 | -0.3009192 | -0.0038227 |
| firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae | -0.1427715 | 0.0722439 | -1.976243 | 0.0485574 | 0.0789058 | -0.2843695 | -0.0011734 |
GAMLSS
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| firmicutes.c__bacilli.o__lactobacillales.f__lactobacillaceae.g__lactobacillus | -0.3315173 | 0.0755929 | -4.385561 | 0.0000135 | 0.0002844 | -0.4796795 | -0.1833552 |
| firmicutes.c__clostridia.oclostridiales.f.g__ | -0.3365252 | 0.0803138 | -4.190128 | 0.0000318 | 0.0003341 | -0.4939403 | -0.1791101 |
| actinobacteria.c__actinobacteria.o__bifidobacteriales.f__bifidobacteriaceae.g__bifidobacterium | 0.2542917 | 0.0712187 | 3.570578 | 0.0003833 | 0.0026828 | 0.1147032 | 0.3938803 |
| firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__.ruminococcus. | -0.2516784 | 0.0741715 | -3.393195 | 0.0007339 | 0.0035457 | -0.3970545 | -0.1063022 |
| bacteroidetes.c__bacteroidia.o__bacteroidales.f__prevotellaceae.g__prevotella | -0.2684274 | 0.0800336 | -3.353932 | 0.0008442 | 0.0035457 | -0.4252933 | -0.1115615 |
| actinobacteria.c__coriobacteriia.o__coriobacteriales.f__coriobacteriaceae.g__ | -0.2173260 | 0.0720564 | -3.016054 | 0.0026637 | 0.0093228 | -0.3585566 | -0.0760954 |
| firmicutes.c__clostridia.o__clostridiales.f__clostridiaceae.g__ | -0.2429816 | 0.0847773 | -2.866116 | 0.0042923 | 0.0128768 | -0.4091452 | -0.0768181 |
| firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__blautia | -0.2191360 | 0.0791422 | -2.768889 | 0.0057874 | 0.0151919 | -0.3742548 | -0.0640173 |
| actinobacteria.c__coriobacteriia.o__coriobacteriales.f__coriobacteriaceae.g__collinsella | -0.1709286 | 0.0682455 | -2.504614 | 0.0125085 | 0.0291864 | -0.3046898 | -0.0371675 |
| firmicutes.c__erysipelotrichi.o__erysipelotrichales.f__erysipelotrichaceae.g__catenibacterium | -0.2297013 | 0.0955240 | -2.404645 | 0.0164716 | 0.0345904 | -0.4169284 | -0.0424743 |
| firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__ | -0.1613206 | 0.0722253 | -2.233574 | 0.0258594 | 0.0493679 | -0.3028823 | -0.0197590 |
| firmicutes.c__bacilli.o__lactobacillales.f__enterococcaceae.g__enterococcus | 0.1801273 | 0.0833351 | 2.161482 | 0.0310272 | 0.0542975 | 0.0167905 | 0.3434641 |
Subramania (Bangladesh) data only.
Only LME was used as GAMLSS has issues with small sample size (when stratifying). LME as showed above has lower power than GAMLSS in general.
In infants with duration of exclusive bf <=2 months
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| actinobacteria.c__actinobacteria.o__bifidobacteriales.f__bifidobacteriaceae | -0.7714898 | 0.1993835 | -3.869376 | 0.0001287 | 0.0016732 | -1.1622815 | -0.3806981 |
| actinobacteria.c__coriobacteriia.o__coriobacteriales.f__coriobacteriaceae | -0.6912195 | 0.1960537 | -3.525664 | 0.0004749 | 0.0030865 | -1.0754847 | -0.3069543 |
| firmicutes.c__bacilli.o__lactobacillales.f__streptococcaceae | 0.5260925 | 0.1836007 | 2.865417 | 0.0043999 | 0.0190660 | 0.1662351 | 0.8859498 |
In infants with duration of exclusive bf >2 months
estimate se teststat pval pval.adjust ll ul ——— — ——— —– ———— — —
GAMLSS
In infants with duration of exclusive bf <=2 months
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| actinobacteria.c__actinobacteria.o__bifidobacteriales.f__bifidobacteriaceae.g__bifidobacterium | -0.7714809 | 0.1993838 | -3.869325 | 0.0001287 | 0.0027034 | -1.1622732 | -0.3806886 |
| firmicutes.c__bacilli.o__lactobacillales.f__streptococcaceae.g__streptococcus | 0.5243671 | 0.1841506 | 2.847491 | 0.0046498 | 0.0488224 | 0.1634320 | 0.8853023 |
| actinobacteria.c__coriobacteriia.o__coriobacteriales.f__coriobacteriaceae.g__collinsella | -0.4992648 | 0.2105904 | -2.370786 | 0.0182565 | 0.1237102 | -0.9120220 | -0.0865075 |
| actinobacteria.c__coriobacteriia.o__coriobacteriales.f__coriobacteriaceae.g__ | -0.4975598 | 0.2188542 | -2.273476 | 0.0235638 | 0.1237102 | -0.9265141 | -0.0686055 |
In infants with duration of exclusive bf >2 months
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| firmicutes.c__clostridia.o__clostridiales.f__lachnospiraceae.g__ | 0.3859128 | 0.2285308 | 1.688668 | 0.0923469 | 0.9809468 | -0.0620076 | 0.8338332 |
In non-exclusive bf infants
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| actinobacteria.c__coriobacteriia.o__coriobacteriales.f__coriobacteriaceae | -0.3440389 | 0.1461708 | -2.353678 | 0.0189040 | 0.2457518 | -0.6305337 | -0.0575442 |
| actinobacteria.c__actinobacteria.o__bifidobacteriales.f__bifidobacteriaceae | -0.2512789 | 0.1516653 | -1.656799 | 0.0980727 | 0.4727405 | -0.5485430 | 0.0459851 |
In no bf infants
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| firmicutes.c__bacilli.o__lactobacillales.f__streptococcaceae | 2.090855 | 0.6246379 | 3.347308 | 0.0017567 | 0.0228374 | 0.8665651 | 3.3151455 |
| actinobacteria.c__actinobacteria.o__bifidobacteriales.f__bifidobacteriaceae | -1.840426 | 0.7653211 | -2.404776 | 0.0207821 | 0.1350835 | -3.3404553 | -0.3403967 |
In bf infants
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| actinobacteria.c__coriobacteriia.o__coriobacteriales.f__coriobacteriaceae.g__collinsella | -0.2910103 | 0.1480753 | -1.965286 | 0.0498330 | 0.654706 | -0.5812379 | -0.0007827 |
| actinobacteria.c__actinobacteria.o__bifidobacteriales.f__bifidobacteriaceae.g__bifidobacterium | -0.2512877 | 0.1516657 | -1.656853 | 0.0980617 | 0.654706 | -0.5485524 | 0.0459770 |
In non-bf infants
| estimate | se | teststat | pval | pval.adjust | ll | ul | |
|---|---|---|---|---|---|---|---|
| firmicutes.c__bacilli.o__lactobacillales.f__streptococcaceae.g__streptococcus | 2.085766 | 0.6249206 | 3.337650 | 0.0018053 | 0.0379113 | 0.8609218 | 3.3106107 |
| actinobacteria.c__actinobacteria.o__bifidobacteriales.f__bifidobacteriaceae.g__bifidobacterium | -1.840411 | 0.7653209 | -2.404758 | 0.0207830 | 0.2182216 | -3.3404403 | -0.3403824 |
With GAMM fit and 95%CI.
GAM part
| Estimate | Std. Error | t value | Pr(>|t|) | |
|---|---|---|---|---|
| (Intercept) | 10.3788398 | 0.2835665 | 36.6010753 | 0.0000000 |
| dia.exbf2No.>2 months | -1.1507899 | 0.4879123 | -2.3585999 | 0.0186104 |
| dia.exbf2Yes.<=2 months | -1.1945958 | 0.4839537 | -2.4684094 | 0.0138028 |
| dia.exbf2Yes.>2 months | -0.5097696 | 0.8117265 | -0.6280066 | 0.5301988 |
| edf | Ref.df | F | p-value | |
|---|---|---|---|---|
| s(age.sample):dia.exbf2No.<=2 months | 5.032806 | 5.032806 | 251.05395 | 0 |
| s(age.sample):dia.exbf2No.>2 months | 4.191756 | 4.191756 | 149.07931 | 0 |
| s(age.sample):dia.exbf2Yes.<=2 months | 1.000000 | 1.000000 | 37.58735 | 0 |
| s(age.sample):dia.exbf2Yes.>2 months | 1.000000 | 1.000000 | 49.79342 | 0 |
LME part
| Value | Std.Error | DF | t-value | p-value | |
|---|---|---|---|---|---|
| X(Intercept) | 10.3788398 | 0.2843456 | 689 | 36.500798 | 0.0000000 |
| Xdia.exbf2No.>2 months | -1.1507899 | 0.4892527 | 689 | -2.352138 | 0.0189463 |
| Xdia.exbf2Yes.<=2 months | -1.1945958 | 0.4852832 | 689 | -2.461647 | 0.0140740 |
| Xdia.exbf2Yes.>2 months | -0.5097696 | 0.8139565 | 689 | -0.626286 | 0.5313348 |
| Xs(age.sample):dia.exbf2No.<=2 monthsFx1 | 1.8308388 | 1.3486999 | 689 | 1.357484 | 0.1750718 |
| Xs(age.sample):dia.exbf2No.>2 monthsFx1 | 1.6657329 | 1.3242074 | 689 | 1.257909 | 0.2088507 |
| Xs(age.sample):dia.exbf2Yes.<=2 monthsFx1 | 3.4720580 | 0.5678815 | 689 | 6.114054 | 0.0000000 |
| Xs(age.sample):dia.exbf2Yes.>2 monthsFx1 | 5.0913209 | 0.7234958 | 689 | 7.037112 | 0.0000000 |
Test for heterogeneity (interaction)
| Estimate | Std. Error | t value | p.val | |
|---|---|---|---|---|
| (Intercept) | 3.7678265 | 0.3316981 | 11.359203 | 0.0000000 |
| age.sample | 0.6832422 | 0.0173814 | 39.308910 | 0.0000000 |
| month.exbf2>2 months | -1.2353814 | 0.5064509 | -2.439291 | 0.0147161 |
| diarrheaYes | -1.0072569 | 0.5024243 | -2.004793 | 0.0449851 |
| month.exbf2>2 months:diarrheaYes | 1.8143024 | 0.9006571 | 2.014421 | 0.0439654 |
With GAMM fit and 95%CI.
| Estimate | Std. Error | t value | Pr(>|t|) | |
|---|---|---|---|---|
| (Intercept) | 3.0665206 | 0.0823202 | 37.2511259 | 0.0000000 |
| dia.exbf2No.>2 months | -0.1567257 | 0.1292484 | -1.2125925 | 0.2255782 |
| dia.exbf2Yes.<=2 months | -0.5837970 | 0.1257959 | -4.6408273 | 0.0000039 |
| dia.exbf2Yes.>2 months | -0.0919724 | 0.1901039 | -0.4838004 | 0.6286357 |
| edf | Ref.df | F | p-value | |
|---|---|---|---|---|
| s(age.sample):dia.exbf2No.<=2 months | 1.000000 | 1.000000 | 511.09021 | 0.00e+00 |
| s(age.sample):dia.exbf2No.>2 months | 5.974811 | 5.974811 | 75.05942 | 0.00e+00 |
| s(age.sample):dia.exbf2Yes.<=2 months | 1.000000 | 1.000000 | 15.96302 | 6.93e-05 |
| s(age.sample):dia.exbf2Yes.>2 months | 1.000000 | 1.000000 | 43.95975 | 0.00e+00 |
| Value | Std.Error | DF | t-value | p-value | |
|---|---|---|---|---|---|
| X(Intercept) | 3.0665206 | 0.0824874 | 935 | 37.175641 | 0.0000000 |
| Xdia.exbf2No.>2 months | -0.1567257 | 0.1295109 | 935 | -1.210135 | 0.2265328 |
| Xdia.exbf2Yes.<=2 months | -0.5837970 | 0.1260513 | 935 | -4.631425 | 0.0000041 |
| Xdia.exbf2Yes.>2 months | -0.0919724 | 0.1904900 | 935 | -0.482820 | 0.6293366 |
| Xs(age.sample):dia.exbf2No.<=2 monthsFx1 | 0.8428954 | 0.0373599 | 935 | 22.561490 | 0.0000000 |
| Xs(age.sample):dia.exbf2No.>2 monthsFx1 | -0.7155803 | 0.5005884 | 935 | -1.429479 | 0.1532008 |
| Xs(age.sample):dia.exbf2Yes.<=2 monthsFx1 | 0.5554706 | 0.1393107 | 935 | 3.987278 | 0.0000720 |
| Xs(age.sample):dia.exbf2Yes.>2 monthsFx1 | 0.9760833 | 0.1475164 | 935 | 6.616780 | 0.0000000 |
GAM part
| Estimate | Std. Error | t value | Pr(>|t|) | |
|---|---|---|---|---|
| (Intercept) | 3.0665206 | 0.0823202 | 37.2511259 | 0.0000000 |
| dia.exbf2No.>2 months | -0.1567257 | 0.1292484 | -1.2125925 | 0.2255782 |
| dia.exbf2Yes.<=2 months | -0.5837970 | 0.1257959 | -4.6408273 | 0.0000039 |
| dia.exbf2Yes.>2 months | -0.0919724 | 0.1901039 | -0.4838004 | 0.6286357 |
| edf | Ref.df | F | p-value | |
|---|---|---|---|---|
| s(age.sample):dia.exbf2No.<=2 months | 1.000000 | 1.000000 | 511.09021 | 0.00e+00 |
| s(age.sample):dia.exbf2No.>2 months | 5.974811 | 5.974811 | 75.05942 | 0.00e+00 |
| s(age.sample):dia.exbf2Yes.<=2 months | 1.000000 | 1.000000 | 15.96302 | 6.93e-05 |
| s(age.sample):dia.exbf2Yes.>2 months | 1.000000 | 1.000000 | 43.95975 | 0.00e+00 |
LME part
| Value | Std.Error | DF | t-value | p-value | |
|---|---|---|---|---|---|
| X(Intercept) | 3.0665206 | 0.0824874 | 935 | 37.175641 | 0.0000000 |
| Xdia.exbf2No.>2 months | -0.1567257 | 0.1295109 | 935 | -1.210135 | 0.2265328 |
| Xdia.exbf2Yes.<=2 months | -0.5837970 | 0.1260513 | 935 | -4.631425 | 0.0000041 |
| Xdia.exbf2Yes.>2 months | -0.0919724 | 0.1904900 | 935 | -0.482820 | 0.6293366 |
| Xs(age.sample):dia.exbf2No.<=2 monthsFx1 | 0.8428954 | 0.0373599 | 935 | 22.561490 | 0.0000000 |
| Xs(age.sample):dia.exbf2No.>2 monthsFx1 | -0.7155803 | 0.5005884 | 935 | -1.429479 | 0.1532008 |
| Xs(age.sample):dia.exbf2Yes.<=2 monthsFx1 | 0.5554706 | 0.1393107 | 935 | 3.987278 | 0.0000720 |
| Xs(age.sample):dia.exbf2Yes.>2 monthsFx1 | 0.9760833 | 0.1475164 | 935 | 6.616780 | 0.0000000 |
Test for heterogeneity (interaction)
| Estimate | Std. Error | t value | p.val | |
|---|---|---|---|---|
| (Intercept) | 1.8029966 | 0.0917394 | 19.653450 | 0.0000000 |
| age.sample | 0.1228124 | 0.0040692 | 30.181133 | 0.0000000 |
| month.exbf2>2 months | -0.1604039 | 0.1316082 | -1.218798 | 0.2229207 |
| diarrheaYes | -0.5210706 | 0.1247534 | -4.176806 | 0.0000296 |
| month.exbf2>2 months:diarrheaYes | 0.5706337 | 0.1973949 | 2.890823 | 0.0038423 |
| Estimate | Std. Error | t value | Pr(>|t|) | |
|---|---|---|---|---|
| (Intercept) | 151.196675 | 8.778134 | 17.2242389 | 0.0000000 |
| dia.exbf2No.>2 months | 6.376610 | 13.831570 | 0.4610185 | 0.6448877 |
| dia.exbf2Yes.<=2 months | -32.741233 | 8.978024 | -3.6468195 | 0.0002795 |
| dia.exbf2Yes.>2 months | 8.288239 | 17.024836 | 0.4868322 | 0.6264862 |
| edf | Ref.df | F | p-value | |
|---|---|---|---|---|
| s(age.sample):dia.exbf2No.<=2 months | 2.241236 | 2.241236 | 186.022933 | 0.0000000 |
| s(age.sample):dia.exbf2No.>2 months | 4.803475 | 4.803475 | 86.288380 | 0.0000000 |
| s(age.sample):dia.exbf2Yes.<=2 months | 1.000000 | 1.000000 | 9.841034 | 0.0017564 |
| s(age.sample):dia.exbf2Yes.>2 months | 1.000000 | 1.000000 | 34.546738 | 0.0000000 |
| Value | Std.Error | DF | t-value | p-value | |
|---|---|---|---|---|---|
| X(Intercept) | 151.196675 | 8.795958 | 935 | 17.1893366 | 0.0000000 |
| Xdia.exbf2No.>2 months | 6.376610 | 13.859654 | 935 | 0.4600843 | 0.6455627 |
| Xdia.exbf2Yes.<=2 months | -32.741233 | 8.996254 | 935 | -3.6394298 | 0.0002882 |
| Xdia.exbf2Yes.>2 months | 8.288239 | 17.059405 | 935 | 0.4858457 | 0.6271904 |
| Xs(age.sample):dia.exbf2No.<=2 monthsFx1 | 51.801469 | 8.730802 | 935 | 5.9331857 | 0.0000000 |
| Xs(age.sample):dia.exbf2No.>2 monthsFx1 | -19.877541 | 26.849174 | 935 | -0.7403409 | 0.4592790 |
| Xs(age.sample):dia.exbf2Yes.<=2 monthsFx1 | 31.121465 | 9.940785 | 935 | 3.1306850 | 0.0017981 |
| Xs(age.sample):dia.exbf2Yes.>2 monthsFx1 | 61.612841 | 10.503858 | 935 | 5.8657345 | 0.0000000 |
GAM part
| Estimate | Std. Error | t value | Pr(>|t|) | |
|---|---|---|---|---|
| (Intercept) | 151.196675 | 8.778134 | 17.2242389 | 0.0000000 |
| dia.exbf2No.>2 months | 6.376610 | 13.831570 | 0.4610185 | 0.6448877 |
| dia.exbf2Yes.<=2 months | -32.741233 | 8.978024 | -3.6468195 | 0.0002795 |
| dia.exbf2Yes.>2 months | 8.288239 | 17.024836 | 0.4868322 | 0.6264862 |
| edf | Ref.df | F | p-value | |
|---|---|---|---|---|
| s(age.sample):dia.exbf2No.<=2 months | 2.241236 | 2.241236 | 186.022933 | 0.0000000 |
| s(age.sample):dia.exbf2No.>2 months | 4.803475 | 4.803475 | 86.288380 | 0.0000000 |
| s(age.sample):dia.exbf2Yes.<=2 months | 1.000000 | 1.000000 | 9.841034 | 0.0017564 |
| s(age.sample):dia.exbf2Yes.>2 months | 1.000000 | 1.000000 | 34.546738 | 0.0000000 |
LME part
| Value | Std.Error | DF | t-value | p-value | |
|---|---|---|---|---|---|
| X(Intercept) | 151.196675 | 8.795958 | 935 | 17.1893366 | 0.0000000 |
| Xdia.exbf2No.>2 months | 6.376610 | 13.859654 | 935 | 0.4600843 | 0.6455627 |
| Xdia.exbf2Yes.<=2 months | -32.741233 | 8.996254 | 935 | -3.6394298 | 0.0002882 |
| Xdia.exbf2Yes.>2 months | 8.288239 | 17.059405 | 935 | 0.4858457 | 0.6271904 |
| Xs(age.sample):dia.exbf2No.<=2 monthsFx1 | 51.801469 | 8.730802 | 935 | 5.9331857 | 0.0000000 |
| Xs(age.sample):dia.exbf2No.>2 monthsFx1 | -19.877541 | 26.849174 | 935 | -0.7403409 | 0.4592790 |
| Xs(age.sample):dia.exbf2Yes.<=2 monthsFx1 | 31.121465 | 9.940785 | 935 | 3.1306850 | 0.0017981 |
| Xs(age.sample):dia.exbf2Yes.>2 monthsFx1 | 61.612841 | 10.503858 | 935 | 5.8657345 | 0.0000000 |
Test for heterogeneity (interaction)
| Estimate | Std. Error | t value | p.val | |
|---|---|---|---|---|
| (Intercept) | 67.218370 | 9.3632479 | 7.1789587 | 0.0000000 |
| age.sample | 8.165080 | 0.2895546 | 28.1987576 | 0.0000000 |
| month.exbf2>2 months | 6.548791 | 14.1631117 | 0.4623836 | 0.6438062 |
| diarrheaYes | -27.156839 | 8.8730060 | -3.0606132 | 0.0022088 |
| month.exbf2>2 months:diarrheaYes | 28.115237 | 14.0092249 | 2.0069088 | 0.0447594 |
| Estimate | Std. Error | t value | Pr(>|t|) | |
|---|---|---|---|---|
| (Intercept) | 11.1473183 | 0.4242502 | 26.2753392 | 0.0000000 |
| dia.exbf2No.>2 months | 0.2157323 | 0.6676390 | 0.3231271 | 0.7466679 |
| dia.exbf2Yes.<=2 months | -2.4295713 | 0.5177632 | -4.6924371 | 0.0000031 |
| dia.exbf2Yes.>2 months | -0.1330212 | 0.8797770 | -0.1511987 | 0.8798500 |
| edf | Ref.df | F | p-value | |
|---|---|---|---|---|
| s(age.sample):dia.exbf2No.<=2 months | 1.00000 | 1.00000 | 651.06494 | 0.0e+00 |
| s(age.sample):dia.exbf2No.>2 months | 4.26171 | 4.26171 | 146.66378 | 0.0e+00 |
| s(age.sample):dia.exbf2Yes.<=2 months | 1.00000 | 1.00000 | 20.80080 | 5.7e-06 |
| s(age.sample):dia.exbf2Yes.>2 months | 1.00000 | 1.00000 | 48.09244 | 0.0e+00 |
| Value | Std.Error | DF | t-value | p-value | |
|---|---|---|---|---|---|
| X(Intercept) | 11.1473183 | 0.4251117 | 935 | 26.2220945 | 0.0000000 |
| Xdia.exbf2No.>2 months | 0.2157323 | 0.6689947 | 935 | 0.3224723 | 0.7471670 |
| Xdia.exbf2Yes.<=2 months | -2.4295713 | 0.5188143 | 935 | -4.6829302 | 0.0000032 |
| Xdia.exbf2Yes.>2 months | -0.1330212 | 0.8815636 | 935 | -0.1508923 | 0.8800932 |
| Xs(age.sample):dia.exbf2No.<=2 monthsFx1 | 3.9257946 | 0.1541688 | 935 | 25.4642659 | 0.0000000 |
| Xs(age.sample):dia.exbf2No.>2 monthsFx1 | 0.5241955 | 1.3248785 | 935 | 0.3956555 | 0.6924494 |
| Xs(age.sample):dia.exbf2Yes.<=2 monthsFx1 | 2.6094784 | 0.5733168 | 935 | 4.5515473 | 0.0000060 |
| Xs(age.sample):dia.exbf2Yes.>2 monthsFx1 | 4.1958246 | 0.6062613 | 935 | 6.9208183 | 0.0000000 |
GAM part
| Estimate | Std. Error | t value | Pr(>|t|) | |
|---|---|---|---|---|
| (Intercept) | 11.1473183 | 0.4242502 | 26.2753392 | 0.0000000 |
| dia.exbf2No.>2 months | 0.2157323 | 0.6676390 | 0.3231271 | 0.7466679 |
| dia.exbf2Yes.<=2 months | -2.4295713 | 0.5177632 | -4.6924371 | 0.0000031 |
| dia.exbf2Yes.>2 months | -0.1330212 | 0.8797770 | -0.1511987 | 0.8798500 |
| edf | Ref.df | F | p-value | |
|---|---|---|---|---|
| s(age.sample):dia.exbf2No.<=2 months | 1.00000 | 1.00000 | 651.06494 | 0.0e+00 |
| s(age.sample):dia.exbf2No.>2 months | 4.26171 | 4.26171 | 146.66378 | 0.0e+00 |
| s(age.sample):dia.exbf2Yes.<=2 months | 1.00000 | 1.00000 | 20.80080 | 5.7e-06 |
| s(age.sample):dia.exbf2Yes.>2 months | 1.00000 | 1.00000 | 48.09244 | 0.0e+00 |
LME part
| Value | Std.Error | DF | t-value | p-value | |
|---|---|---|---|---|---|
| X(Intercept) | 11.1473183 | 0.4251117 | 935 | 26.2220945 | 0.0000000 |
| Xdia.exbf2No.>2 months | 0.2157323 | 0.6689947 | 935 | 0.3224723 | 0.7471670 |
| Xdia.exbf2Yes.<=2 months | -2.4295713 | 0.5188143 | 935 | -4.6829302 | 0.0000032 |
| Xdia.exbf2Yes.>2 months | -0.1330212 | 0.8815636 | 935 | -0.1508923 | 0.8800932 |
| Xs(age.sample):dia.exbf2No.<=2 monthsFx1 | 3.9257946 | 0.1541688 | 935 | 25.4642659 | 0.0000000 |
| Xs(age.sample):dia.exbf2No.>2 monthsFx1 | 0.5241955 | 1.3248785 | 935 | 0.3956555 | 0.6924494 |
| Xs(age.sample):dia.exbf2Yes.<=2 monthsFx1 | 2.6094784 | 0.5733168 | 935 | 4.5515473 | 0.0000060 |
| Xs(age.sample):dia.exbf2Yes.>2 monthsFx1 | 4.1958246 | 0.6062613 | 935 | 6.9208183 | 0.0000000 |
Test for heterogeneity (interaction)
| Estimate | Std. Error | t value | p.val | |
|---|---|---|---|---|
| (Intercept) | 5.1010594 | 0.4591138 | 11.1106653 | 0.0000000 |
| age.sample | 0.5894225 | 0.0166254 | 35.4531752 | 0.0000000 |
| month.exbf2>2 months | 0.2033228 | 0.6822247 | 0.2980291 | 0.7656809 |
| diarrheaYes | -2.1261538 | 0.5095509 | -4.1726032 | 0.0000301 |
| month.exbf2>2 months:diarrheaYes | 1.7538795 | 0.8050786 | 2.1785195 | 0.0293674 |
| Estimate | Std. Error | t value | Pr(>|t|) | |
|---|---|---|---|---|
| (Intercept) | 367.19115 | 24.93875 | 14.7237215 | 0.0000000 |
| dia.exbf2No.>2 months | 16.36035 | 39.31689 | 0.4161151 | 0.6774169 |
| dia.exbf2Yes.<=2 months | -86.62794 | 23.43335 | -3.6967801 | 0.0002305 |
| dia.exbf2Yes.>2 months | 28.78746 | 47.08230 | 0.6114285 | 0.5410577 |
| edf | Ref.df | F | p-value | |
|---|---|---|---|---|
| s(age.sample):dia.exbf2No.<=2 months | 1.502023 | 1.502023 | 261.413376 | 0.0000000 |
| s(age.sample):dia.exbf2No.>2 months | 4.677640 | 4.677640 | 76.504447 | 0.0000000 |
| s(age.sample):dia.exbf2Yes.<=2 months | 1.000000 | 1.000000 | 7.810505 | 0.0052936 |
| s(age.sample):dia.exbf2Yes.>2 months | 1.000000 | 1.000000 | 29.909461 | 0.0000001 |
| Value | Std.Error | DF | t-value | p-value | |
|---|---|---|---|---|---|
| X(Intercept) | 367.19115 | 24.98938 | 935 | 14.6938872 | 0.0000000 |
| Xdia.exbf2No.>2 months | 16.36035 | 39.39672 | 935 | 0.4152720 | 0.6780381 |
| Xdia.exbf2Yes.<=2 months | -86.62794 | 23.48093 | 935 | -3.6892894 | 0.0002379 |
| Xdia.exbf2Yes.>2 months | 28.78746 | 47.17789 | 935 | 0.6101897 | 0.5418844 |
| Xs(age.sample):dia.exbf2No.<=2 monthsFx1 | 134.05173 | 12.55943 | 935 | 10.6733923 | 0.0000000 |
| Xs(age.sample):dia.exbf2No.>2 monthsFx1 | -43.96611 | 67.65832 | 935 | -0.6498257 | 0.5159644 |
| Xs(age.sample):dia.exbf2Yes.<=2 monthsFx1 | 72.36395 | 25.94559 | 935 | 2.7890649 | 0.0053934 |
| Xs(age.sample):dia.exbf2Yes.>2 monthsFx1 | 149.59600 | 27.40922 | 935 | 5.4578722 | 0.0000001 |
GAM part
| Estimate | Std. Error | t value | Pr(>|t|) | |
|---|---|---|---|---|
| (Intercept) | 367.19115 | 24.93875 | 14.7237215 | 0.0000000 |
| dia.exbf2No.>2 months | 16.36035 | 39.31689 | 0.4161151 | 0.6774169 |
| dia.exbf2Yes.<=2 months | -86.62794 | 23.43335 | -3.6967801 | 0.0002305 |
| dia.exbf2Yes.>2 months | 28.78746 | 47.08230 | 0.6114285 | 0.5410577 |
| edf | Ref.df | F | p-value | |
|---|---|---|---|---|
| s(age.sample):dia.exbf2No.<=2 months | 1.502023 | 1.502023 | 261.413376 | 0.0000000 |
| s(age.sample):dia.exbf2No.>2 months | 4.677640 | 4.677640 | 76.504447 | 0.0000000 |
| s(age.sample):dia.exbf2Yes.<=2 months | 1.000000 | 1.000000 | 7.810505 | 0.0052936 |
| s(age.sample):dia.exbf2Yes.>2 months | 1.000000 | 1.000000 | 29.909461 | 0.0000001 |
LME part
| Value | Std.Error | DF | t-value | p-value | |
|---|---|---|---|---|---|
| X(Intercept) | 367.19115 | 24.98938 | 935 | 14.6938872 | 0.0000000 |
| Xdia.exbf2No.>2 months | 16.36035 | 39.39672 | 935 | 0.4152720 | 0.6780381 |
| Xdia.exbf2Yes.<=2 months | -86.62794 | 23.48093 | 935 | -3.6892894 | 0.0002379 |
| Xdia.exbf2Yes.>2 months | 28.78746 | 47.17789 | 935 | 0.6101897 | 0.5418844 |
| Xs(age.sample):dia.exbf2No.<=2 monthsFx1 | 134.05173 | 12.55943 | 935 | 10.6733923 | 0.0000000 |
| Xs(age.sample):dia.exbf2No.>2 monthsFx1 | -43.96611 | 67.65832 | 935 | -0.6498257 | 0.5159644 |
| Xs(age.sample):dia.exbf2Yes.<=2 monthsFx1 | 72.36395 | 25.94559 | 935 | 2.7890649 | 0.0053934 |
| Xs(age.sample):dia.exbf2Yes.>2 monthsFx1 | 149.59600 | 27.40922 | 935 | 5.4578722 | 0.0000001 |
Test for heterogeneity (interaction)
| Estimate | Std. Error | t value | p.val | |
|---|---|---|---|---|
| (Intercept) | 161.48642 | 26.4705453 | 6.1006078 | 0.0000000 |
| age.sample | 20.00874 | 0.7538543 | 26.5419213 | 0.0000000 |
| month.exbf2>2 months | 16.28471 | 40.3235504 | 0.4038512 | 0.6863222 |
| diarrheaYes | -72.27871 | 23.0991493 | -3.1290636 | 0.0017536 |
| month.exbf2>2 months:diarrheaYes | 83.14805 | 36.4602574 | 2.2805118 | 0.0225774 |
Combined graph
R session information
R version 3.4.2 (2017-09-28)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] gplots_3.0.1 bindrcpp_0.2 meta_4.9-0
[4] randomForest_4.6-12 gdata_2.18.0 scales_0.5.0
[7] RColorBrewer_1.1-2 geepack_1.2-1 zoo_1.8-0
[10] itsadug_2.3 plotfunctions_1.3 mgcv_1.8-22
[13] nlme_3.1-131 reshape2_1.4.3 lmerTest_2.0-36
[16] sjPlot_2.4.0 sjmisc_2.6.3 lme4_1.1-15
[19] Matrix_1.2-12 tidyr_0.7.2 dtplyr_0.0.2
[22] data.table_1.10.4-3 dplyr_0.7.4 date_1.2-37
[25] lubridate_1.7.1 chron_2.3-51 gmodels_2.16.2
[28] gridExtra_2.3 plyr_1.8.4 digest_0.6.12
[31] caret_6.0-78 ggplot2_2.2.1 lattice_0.20-35
[34] knitr_1.17
loaded via a namespace (and not attached):
[1] backports_1.1.1 Hmisc_4.0-3 blme_1.0-4
[4] lazyeval_0.2.1 TMB_1.7.11 splines_3.4.2
[7] TH.data_1.0-8 foreach_1.4.3 htmltools_0.3.6
[10] magrittr_1.5 checkmate_1.8.5 cluster_2.0.6
[13] sfsmisc_1.1-1 recipes_0.1.1 modelr_0.1.1
[16] gower_0.1.2 dimRed_0.1.0 sandwich_2.4-0
[19] colorspace_1.3-2 haven_1.1.0 crayon_1.3.4
[22] bindr_0.1 survival_2.41-3 iterators_1.0.8
[25] glue_1.2.0 DRR_0.0.2 gtable_0.2.0
[28] ipred_0.9-6 sjstats_0.13.0 kernlab_0.9-25
[31] ddalpha_1.3.1 DEoptimR_1.0-8 abind_1.4-5
[34] mvtnorm_1.0-6 ggeffects_0.3.0 Rcpp_0.12.14
[37] xtable_1.8-2 merTools_0.3.0 htmlTable_1.11.0
[40] foreign_0.8-69 Formula_1.2-2 stats4_3.4.2
[43] prediction_0.2.0 lava_1.5.1 survey_3.32-1
[46] prodlim_1.6.1 DT_0.2 htmlwidgets_0.9
[49] acepack_1.4.1 modeltools_0.2-21 pkgconfig_2.0.1
[52] nnet_7.3-12 labeling_0.3 tidyselect_0.2.3
[55] rlang_0.1.4 munsell_0.4.3 tools_3.4.2
[58] cli_1.0.0 sjlabelled_1.0.5 broom_0.4.3
[61] evaluate_0.10.1 stringr_1.2.0 arm_1.9-3
[64] yaml_2.1.15 ModelMetrics_1.1.0 robustbase_0.92-8
[67] caTools_1.17.1 purrr_0.2.4 coin_1.2-2
[70] mime_0.5 RcppRoll_0.2.2 compiler_3.4.2
[73] bayesplot_1.4.0 rstudioapi_0.7.0-9000 tibble_1.3.4
[76] stringi_1.1.6 highr_0.6 forcats_0.2.0
[79] psych_1.7.8 nloptr_1.0.4 effects_4.0-0
[82] stringdist_0.9.4.6 pwr_1.2-1 lmtest_0.9-35
[85] bitops_1.0-6 httpuv_1.3.5 R6_2.2.2
[88] latticeExtra_0.6-28 KernSmooth_2.23-15 codetools_0.2-15
[91] MASS_7.3-47 gtools_3.5.0 assertthat_0.2.0
[94] CVST_0.2-1 rprojroot_1.2 withr_2.1.0
[97] mnormt_1.5-5 multcomp_1.4-8 parallel_3.4.2
[100] grid_3.4.2 rpart_4.1-11 timeDate_3042.101
[103] coda_0.19-1 glmmTMB_0.2.0 class_7.3-14
[106] minqa_1.2.4 rmarkdown_1.8 snakecase_0.5.1
[109] carData_3.0-0 shiny_1.0.5 base64enc_0.1-3